Mercurial > repos > artbio > varscan_vaf
changeset 0:0b6ec297a6bc draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/varscan_vaf commit ff9426700b78da43ad64bf4905d358ee4986127b
| author | artbio |
|---|---|
| date | Mon, 28 Nov 2022 21:59:34 +0000 |
| parents | |
| children | |
| files | test-data/computed_VAFs_1.vcf test-data/computed_VAFs_2.vcf test-data/vcf_1.vcf test-data/vcf_2.vcf varscan_vaf.py varscan_vaf.xml |
| diffstat | 6 files changed, 983 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/computed_VAFs_1.vcf Mon Nov 28 21:59:34 2022 +0000 @@ -0,0 +1,189 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=PASS,Description="All filters passed"> +##reference=/home/galaxy/galaxy/tool-data/hg38-bgi-light/sam_indexes/hg38-bgi-light/hg38-bgi-light.fa +##source=varscan.py +##contig=<ID=chr1,length=248956422> +##contig=<ID=chr10,length=133797422> +##contig=<ID=chr11,length=135086622> +##contig=<ID=chr12,length=133275309> +##contig=<ID=chr13,length=114364328> +##contig=<ID=chr14,length=107043718> +##contig=<ID=chr15,length=101991189> +##contig=<ID=chr16,length=90338345> +##contig=<ID=chr17,length=83257441> +##contig=<ID=chr18,length=80373285> +##contig=<ID=chr19,length=58617616> +##contig=<ID=chr2,length=242193529> +##contig=<ID=chr20,length=64444167> +##contig=<ID=chr21,length=46709983> +##contig=<ID=chr22,length=50818468> +##contig=<ID=chr3,length=198295559> +##contig=<ID=chr4,length=190214555> +##contig=<ID=chr5,length=181538259> +##contig=<ID=chr6,length=170805979> +##contig=<ID=chr7,length=159345973> +##contig=<ID=chr8,length=145138636> +##contig=<ID=chr9,length=138394717> +##contig=<ID=chrM,length=16569> +##contig=<ID=chrX,length=156040895> +##contig=<ID=chrY,length=57227415> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases"> +##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation"> +##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)"> +##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value"> +##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls"> +##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls"> +##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand"> +##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position"> +##FILTER=<ID=VarCount,Description="Fewer than 4 variant-supporting reads"> +##FILTER=<ID=VarFreq,Description="Variant allele frequency below 0.05"> +##FILTER=<ID=VarAvgRL,Description="Average clipped length of variant-supporting reads < 90"> +##FILTER=<ID=VarReadPos,Description="Relative average read position < 0.1"> +##FILTER=<ID=VarDist3,Description="Average distance to effective 3' end < 0.1"> +##FILTER=<ID=VarMMQS,Description="Average mismatch quality sum for variant reads > 100"> +##FILTER=<ID=VarMapQual,Description="Average mapping quality of variant reads < 15"> +##FILTER=<ID=VarBaseQual,Description="Average base quality of variant reads < 15"> +##FILTER=<ID=Strand,Description="Strand representation of variant reads < 0.01"> +##FILTER=<ID=RefAvgRL,Description="Average clipped length of ref-supporting reads < 90"> +##FILTER=<ID=RefReadPos,Description="Relative average read position < 0.1"> +##FILTER=<ID=RefDist3,Description="Average distance to effective 3' end < 0.1"> +##FILTER=<ID=RefMapQual,Description="Average mapping quality of reference reads < 15"> +##FILTER=<ID=RefBaseQual,Description="Average base quality of ref-supporting reads < 15"> +##FILTER=<ID=RefMMQS,Description="Average mismatch quality sum for ref-supporting reads > 100"> +##FILTER=<ID=MMQSdiff,Description="Mismatch quality sum difference (var - ref) > 50"> +##FILTER=<ID=MinMMQSdiff,Description="Mismatch quality sum difference (var - ref) < 50"> +##FILTER=<ID=MapQualDiff,Description="Mapping quality difference (ref - var) > 50"> +##FILTER=<ID=MaxBAQdiff,Description="Average base quality difference (ref - var) > 50"> +##FILTER=<ID=ReadLenDiff,Description="Average supporting read length difference (ref - var) > 0.25"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype code"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth"> +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele"> +##FORMAT=<ID=ADF,Number=R,Type=Integer,Description="Read depth for each allele on the forward strand"> +##FORMAT=<ID=ADR,Number=R,Type=Integer,Description="Read depth for each allele on the reverse strand"> +##bcftools_filterVersion=1.10.2+htslib-1.10.2 +##bcftools_filterCommand=filter --include 'INFO/SPV < 0.12 | INFO/GPV < 0.12' --output-type v --threads 1 input.vcf.gz; Date=Thu Apr 21 00:18:01 2022 +##bcftools_filterCommand=filter --include 'FILTER ~ "PASS" | FILTER ~ "MinMMQSdiff" | FILTER ~ "RefReadPos"' --output-type v --threads 1 input.vcf.gz; Date=Wed Sep 7 20:48:58 2022 +##bcftools_viewVersion=1.10.2+htslib-1.10.2 +##bcftools_viewCommand=view --output-type v; Date=Wed Sep 7 20:49:09 2022 +##bcftools_filterCommand=filter --include 'INFO/SS ~ "2"' --output-type v --threads 1 input.vcf.gz; Date=Wed Sep 7 20:49:20 2022 +##SnpSiftVersion="SnpSift 4.3t (build 2017-11-24 10:18), by Pablo Cingolani" +##SnpSiftCmd="SnpSift Annotate -info GENEINFO,PSEUDOGENEINFO,SAO,SSR,VC,NSF,NSM,NSN,SYN,U3,U5,ASS,DSS,INT,R3,R5,FREQ,COMMON,CLNVI,CLNORIGIN,CLNSIG,CLNDISDB,CLNDN,CLNREVSTAT,CLNACC dbSnp.vcf /home/galaxy/galaxy/database/datasets/001/336/dataset_1336143.dat" +##INFO=<ID=NSF,Number=0,Type=Flag,Description="Has non-synonymous frameshift A coding region variation where one allele in the set changes all downstream amino acids. FxnClass = 44"> +##INFO=<ID=R3,Number=0,Type=Flag,Description="In 3' gene region FxnCode = 13"> +##INFO=<ID=R5,Number=0,Type=Flag,Description="In 5' gene region FxnCode = 15"> +##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Variant Clinical Significance, 0 - Uncertain significance, 1 - not provided, 2 - Benign, 3 - Likely benign, 4 - Likely pathogenic, 5 - Pathogenic, 6 - drug response, 8 - confers sensitivity, 9 - risk-factor, 10 - association, 11 - protective, 12 - conflict, 13 - affects, 255 - other"> +##INFO=<ID=NSN,Number=0,Type=Flag,Description="Has non-synonymous nonsense A coding region variation where one allele in the set changes to STOP codon (TER). FxnClass = 41"> +##INFO=<ID=NSM,Number=0,Type=Flag,Description="Has non-synonymous missense A coding region variation where one allele in the set changes protein peptide. FxnClass = 42"> +##INFO=<ID=CLNORIGIN,Number=.,Type=String,Description="Allele Origin. One or more of the following values may be summed: 0 - unknown; 1 - germline; 2 - somatic; 4 - inherited; 8 - paternal; 16 - maternal; 32 - de-novo; 64 - biparental; 128 - uniparental; 256 - not-tested; 512 - tested-inconclusive; 1073741824 - other"> +##INFO=<ID=CLNREVSTAT,Number=.,Type=String,Description="ClinVar Review Status: no_assertion - No asserition provided by submitter, no_criteria - No assertion criteria provided by submitter, single - Classified by single submitter, mult - Classified by multiple submitters, conf - Criteria provided conflicting interpretations, exp - Reviewed by expert panel, guideline - Practice guideline"> +##INFO=<ID=COMMON,Number=0,Type=Flag,Description="RS is a common SNP. A common SNP is one that has at least one 1000Genomes population with a minor allele of frequency >= 1% and for which 2 or more founders contribute to that minor allele frequency."> +##INFO=<ID=FREQ,Number=.,Type=String,Description="An ordered list of allele frequencies as reported by various genomic studies starting with the reference allele followed by alternate alleles as ordered in the ALT column. When not already in the dbSNP allele set alleles from the studies are added to the ALT column. The minor allele which was previuosly reported in VCF as the GMAF is the second largest value in the list. This is the GMAF reported on the RefSNP and EntrezSNP pages and VariationReporter"> +##INFO=<ID=ASS,Number=0,Type=Flag,Description="In acceptor splice site FxnCode = 73"> +##INFO=<ID=U3,Number=0,Type=Flag,Description="In 3' UTR Location is in an untranslated region (UTR). FxnCode = 53"> +##INFO=<ID=U5,Number=0,Type=Flag,Description="In 5' UTR Location is in an untranslated region (UTR). FxnCode = 55"> +##INFO=<ID=CLNACC,Number=.,Type=String,Description="For each allele (comma delimited), this is a pipe-delimited list of the Clinvar RCV phenotype accession.version strings associated with that allele."> +##INFO=<ID=CLNDN,Number=.,Type=String,Description="Preferred ClinVar disease name"> +##INFO=<ID=DSS,Number=0,Type=Flag,Description="In donor splice-site FxnCode = 75"> +##INFO=<ID=SYN,Number=0,Type=Flag,Description="Has synonymous A coding region variation where one allele in the set does not change the encoded amino acid. FxnCode = 3"> +##INFO=<ID=CLNVI,Number=.,Type=String,Description="Variant Identifiers provided and maintained by organizations outside of NCBI, such as OMIM. Source and id separated by colon (:). Each identifier is separated by a vertical bar (|)"> +##INFO=<ID=VC,Number=1,Type=String,Description="Variation Class"> +##INFO=<ID=SAO,Number=1,Type=Integer,Description="Variant Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both"> +##INFO=<ID=PSEUDOGENEINFO,Number=1,Type=String,Description="Pairs each of pseudogene symbol:gene id. The pseudogene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|)"> +##INFO=<ID=CLNDISDB,Number=.,Type=String,Description="Variant disease database name and ID, separated by colon (:)"> +##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|). Does not include pseudogenes."> +##INFO=<ID=INT,Number=0,Type=Flag,Description="In Intron FxnCode = 6"> +##INFO=<ID=SSR,Number=1,Type=Integer,Description="Variant Suspect Reason Codes (may be more than one value added together) 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other"> +##bcftools_concatVersion=1.10.2+htslib-1.10.2 +##bcftools_concatCommand=concat --allow-overlaps --min-PQ 30 --output-type v --threads 1 input0.vcf.gz input1.vcf.gz input2.vcf.gz input3.vcf.gz input4.vcf.gz input5.vcf.gz input6.vcf.gz input7.vcf.gz input8.vcf.gz input9.vcf.gz input10.vcf.gz input11.vcf.gz input12.vcf.gz input13.vcf.gz input14.vcf.gz input15.vcf.gz input16.vcf.gz input17.vcf.gz input18.vcf.gz input19.vcf.gz input20.vcf.gz input21.vcf.gz input22.vcf.gz input23.vcf.gz input24.vcf.gz; Date=Wed Sep 7 20:53:30 2022 +##bcftools_filterCommand=filter --include 'INFO/COMMON = 0' --output-type v --threads 1 input.vcf.gz; Date=Wed Sep 7 20:53:35 2022 +##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani" +##SnpEffCmd="SnpEff -i vcf -o vcf -stats /home/galaxy/galaxy/database/datasets/001/336/dataset_1336196.dat hg38 /home/galaxy/galaxy/database/datasets/001/336/dataset_1336194.dat " +##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'"> +##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +##INFO=<ID=ANNOVAR_DATE,Number=1,Type=String,Description="Flag the start of ANNOVAR annotation for one alternative allele"> +##INFO=<ID=cosmic70,Number=.,Type=String,Description="cosmic70 annotation provided by ANNOVAR"> +##INFO=<ID=SIFT_score,Number=.,Type=String,Description="SIFT_score annotation provided by ANNOVAR"> +##INFO=<ID=SIFT_pred,Number=.,Type=String,Description="SIFT_pred annotation provided by ANNOVAR"> +##INFO=<ID=Polyphen2_HDIV_score,Number=.,Type=String,Description="Polyphen2_HDIV_score annotation provided by ANNOVAR"> +##INFO=<ID=Polyphen2_HDIV_pred,Number=.,Type=String,Description="Polyphen2_HDIV_pred annotation provided by ANNOVAR"> +##INFO=<ID=Polyphen2_HVAR_score,Number=.,Type=String,Description="Polyphen2_HVAR_score annotation provided by ANNOVAR"> +##INFO=<ID=Polyphen2_HVAR_pred,Number=.,Type=String,Description="Polyphen2_HVAR_pred annotation provided by ANNOVAR"> +##INFO=<ID=LRT_score,Number=.,Type=String,Description="LRT_score annotation provided by ANNOVAR"> +##INFO=<ID=LRT_pred,Number=.,Type=String,Description="LRT_pred annotation provided by ANNOVAR"> +##INFO=<ID=MutationTaster_score,Number=.,Type=String,Description="MutationTaster_score annotation provided by ANNOVAR"> +##INFO=<ID=MutationTaster_pred,Number=.,Type=String,Description="MutationTaster_pred annotation provided by ANNOVAR"> +##INFO=<ID=MutationAssessor_score,Number=.,Type=String,Description="MutationAssessor_score annotation provided by ANNOVAR"> +##INFO=<ID=MutationAssessor_pred,Number=.,Type=String,Description="MutationAssessor_pred annotation provided by ANNOVAR"> +##INFO=<ID=FATHMM_score,Number=.,Type=String,Description="FATHMM_score annotation provided by ANNOVAR"> +##INFO=<ID=FATHMM_pred,Number=.,Type=String,Description="FATHMM_pred annotation provided by ANNOVAR"> +##INFO=<ID=RadialSVM_score,Number=.,Type=String,Description="RadialSVM_score annotation provided by ANNOVAR"> +##INFO=<ID=RadialSVM_pred,Number=.,Type=String,Description="RadialSVM_pred annotation provided by ANNOVAR"> +##INFO=<ID=LR_score,Number=.,Type=String,Description="LR_score annotation provided by ANNOVAR"> +##INFO=<ID=LR_pred,Number=.,Type=String,Description="LR_pred annotation provided by ANNOVAR"> +##INFO=<ID=VEST3_score,Number=.,Type=String,Description="VEST3_score annotation provided by ANNOVAR"> +##INFO=<ID=CADD_raw,Number=.,Type=String,Description="CADD_raw annotation provided by ANNOVAR"> +##INFO=<ID=CADD_phred,Number=.,Type=String,Description="CADD_phred annotation provided by ANNOVAR"> +##INFO=<ID=GERP++_RS,Number=.,Type=String,Description="GERP++_RS annotation provided by ANNOVAR"> +##INFO=<ID=phyloP46way_placental,Number=.,Type=String,Description="phyloP46way_placental annotation provided by ANNOVAR"> +##INFO=<ID=phyloP100way_vertebrate,Number=.,Type=String,Description="phyloP100way_vertebrate annotation provided by ANNOVAR"> +##INFO=<ID=SiPhy_29way_logOdds,Number=.,Type=String,Description="SiPhy_29way_logOdds annotation provided by ANNOVAR"> +##INFO=<ID=CLNALLELEID,Number=.,Type=String,Description="CLNALLELEID annotation provided by ANNOVAR"> +##INFO=<ID=ALLELE_END,Number=0,Type=Flag,Description="Flag the end of ANNOVAR annotation for one alternative allele"> +##bcftools_filterCommand=filter --include 'INFO/LOF != "." | INFO/CLNSIG != "." | INFO/cosmic70 != "." | INFO/Polyphen2_HDIV_pred != "." | INFO/LRT_pred != "." | INFO/MutationTaster_pred != "." | INFO/MutationAssessor_pred != "." | INFO/FATHMM_pred != "."' --output-type v --threads 1 input.vcf.gz; Date=Wed Sep 7 20:55:15 2022 +##SnpEffCmd="SnpEff -i vcf -o vcf -stats /home/galaxy/galaxy/database/datasets/001/336/dataset_1336200.dat hg38 /home/galaxy/galaxy/database/datasets/001/336/dataset_1336198.dat " +##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' "> +##FORMAT=<ID=VAF,Number=R,Type=float,Description="VariantAllele Frequency"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 01002_normal 01002_tumor +chr1 42536528 . AAG A . MinMMQSdiff DP=160;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10106;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=ID\x3dCOSM391243\x3bOCCURENCE\x3d1(lung),1(pancreas),4(large_intestine);SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=A|frameshift_variant|HIGH|CCDC30|CCDC30|transcript|NM_001080850.2|protein_coding|2/16|c.60_61delGA|p.Lys21fs|170/3098|60/2352|20/783||INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:50:50,0:26,0:24,0:0.000 0/1:.:110:104,6:56,2:48,4:0.055 +chr1 100206310 . TA T . MinMMQSdiff DP=144;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.1157;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=433480;CLNDN=Maple_syrup_urine_disease|not_specified;CLNDISDB=MONDO:MONDO:0009563,MeSH:D008375,MedGen:C0024776,OMIM:248600,OMIM:PS248600,Orphanet:ORPHA511,SNOMED_CT:27718001|MedGen:CN169374;CLNREVSTAT=criteria_provided,_multiple_submitters,_no_conflicts;CLNSIG=Benign;ALLELE_END;ANN=T|intron_variant|MODIFIER|DBT|DBT|transcript|NM_001918.3|protein_coding|9/10|c.1210-10delT|||||| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:42:40,0:23,0:17,0:0.000 0/1:.:102:89,6:54,3:35,3:0.063 +chr1 100539628 . T C . PASS DP=18;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.068627;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.77;SIFT_pred=T;Polyphen2_HDIV_score=0.386;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.157;Polyphen2_HVAR_pred=B;LRT_score=0.119;LRT_pred=U;MutationTaster_score=0.982;MutationTaster_pred=N;MutationAssessor_score=0;MutationAssessor_pred=N;FATHMM_score=1.27;FATHMM_pred=T;RadialSVM_score=-0.979;RadialSVM_pred=T;LR_score=0.014;LR_pred=T;VEST3_score=0.371;CADD_raw=-1.497;CADD_phred=0.017;GERP++_RS=2.92;phyloP46way_placental=1.237;phyloP100way_vertebrate=1.470;SiPhy_29way_logOdds=8.418;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|GPR88|GPR88|transcript|NM_022049.2|protein_coding|2/2|c.662T>C|p.Val221Ala|1066/3465|662/1155|221/384|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:10:10,0:8,0:2,0:0.000 0/1:.:8:5,3:0,0:5,3:0.375 +chr1 112912805 . TA T . PASS DP=142;SOMATIC;SS=2;SSC=14;GPV=1;SPV=0.039564;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=276120;CLNDN=Hyperinsulinism,_Dominant;CLNDISDB=MedGen:CN239341;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Uncertain_significance;ALLELE_END;ANN=T|3_prime_UTR_variant|MODIFIER|SLC16A1|SLC16A1|transcript|NM_001166496.1|protein_coding|5/5|c.*1085delT|||||1085|,T|3_prime_UTR_variant|MODIFIER|SLC16A1|SLC16A1|transcript|NM_003051.3|protein_coding|5/5|c.*1085delT|||||1085| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:43:43,0:22,0:21,0:0.000 0/1:.:99:82,8:45,7:37,1:0.089 +chr1 151088217 . T G . PASS DP=134;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11875;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.01;SIFT_pred=D;Polyphen2_HDIV_score=0.999;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.977;Polyphen2_HVAR_pred=D;LRT_score=0.000;LRT_pred=D;MutationTaster_score=0.996;MutationTaster_pred=D;MutationAssessor_score=2.48;MutationAssessor_pred=M;FATHMM_score=-0.17;FATHMM_pred=T;RadialSVM_score=-0.479;RadialSVM_pred=T;LR_score=0.294;LR_pred=T;VEST3_score=0.897;CADD_raw=4.062;CADD_phred=20.9;GERP++_RS=0.551;phyloP46way_placental=0.181;phyloP100way_vertebrate=0.031;SiPhy_29way_logOdds=9.216;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_001323910.1|protein_coding|2/10|c.28T>G|p.Leu10Val|385/2027|28/1395|10/464||,G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_001323907.1|protein_coding|2/8|c.28T>G|p.Leu10Val|385/1745|28/1113|10/370||,G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_001323908.1|protein_coding|2/9|c.28T>G|p.Leu10Val|417/2011|28/1347|10/448||,G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_001323909.1|protein_coding|2/8|c.28T>G|p.Leu10Val|385/1865|28/1233|10/410||,G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_001323912.1|protein_coding|3/8|c.28T>G|p.Leu10Val|504/1816|28/1065|10/354||,G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_001323913.1|protein_coding|2/8|c.28T>G|p.Leu10Val|385/1811|28/1179|10/392||,G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_001323906.1|protein_coding|2/10|c.28T>G|p.Leu10Val|385/2946|28/1359|10/452||,G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_001323911.1|protein_coding|2/9|c.28T>G|p.Leu10Val|385/2832|28/1245|10/414||,G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_144618.2|protein_coding|2/9|c.28T>G|p.Leu10Val|359/1953|28/1347|10/448|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:39:39,0:18,0:21,0:0.000 0/1:.:95:88,6:48,5:40,1:0.064 +chr1 193251844 . G GT . MinMMQSdiff DP=181;SOMATIC;SS=2;SSC=14;GPV=1;SPV=0.039165;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=279150;CLNDN=Parathyroid_carcinoma|Hyperparathyroidism_2|Isolated_Hyperparathyroidism;CLNDISDB=Human_Phenotype_Ontology:HP:0006780,MONDO:MONDO:0012004,MedGen:C0687150,OMIM:608266,Orphanet:ORPHA143,SNOMED_CT:255037004|MONDO:MONDO:0007768,MedGen:C1704981,OMIM:145001,Orphanet:ORPHA99880|MedGen:CN239442;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Uncertain_significance;ALLELE_END;ANN=GT|3_prime_UTR_variant|MODIFIER|CDC73|CDC73|transcript|NM_024529.4|protein_coding|17/17|c.*1144dupT|||||1145|INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:49:48,0:23,0:25,0:0.000 0/1:.:132:120,10:60,4:60,6:0.077 +chr1 197090091 . G GA . MinMMQSdiff DP=139;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.073566;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=193063;CLNDN=not_provided;CLNDISDB=MedGen:CN517202;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Uncertain_significance;ALLELE_END;ANN=GA|splice_region_variant&intron_variant|LOW|ASPM|ASPM|transcript|NM_018136.4|protein_coding|24/27|c.9830-8dupT||||||,GA|splice_region_variant&intron_variant|LOW|ASPM|ASPM|transcript|NM_001206846.1|protein_coding|23/26|c.5075-8dupT|||||| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:42:42,0:22,0:20,0:0.000 0/1:.:97:89,7:56,5:33,2:0.073 +chr1 215741541 . G GA . MinMMQSdiff DP=159;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.09137;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=195468;CLNDN=not_specified;CLNDISDB=MedGen:CN169374;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;ALLELE_END;ANN=GA|splice_region_variant&intron_variant|LOW|USH2A|USH2A|transcript|NM_206933.2|protein_coding|59/71|c.11549-5dupT|||||| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:46:44,0:20,0:24,0:0.000 0/1:.:113:104,7:59,3:45,4:0.063 +chr1 247949492 rs200574966 G C . MinMMQSdiff DP=58;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.076494;FREQ=ExAC:0.9999,.,9.101e-05|GnomAD_exomes:1,.,1.196e-05|KOREAN:0.9798,.,0.02019|TOMMO:0.9837,.,0.01629|dbGaP_PopFreq:0.9983,0,0.001659;GENEINFO=OR2L13:284521|OR2L8:391190;INT;NSM;R5;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.11;SIFT_pred=T;Polyphen2_HDIV_score=0.001;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.021;Polyphen2_HVAR_pred=B;LRT_score=0.447;LRT_pred=U;MutationTaster_score=1.000;MutationTaster_pred=N;MutationAssessor_score=-0.13;MutationAssessor_pred=N;FATHMM_score=1.28;FATHMM_pred=T;RadialSVM_score=-1.057;RadialSVM_pred=T;LR_score=0.035;LR_pred=T;VEST3_score=0.097;CADD_raw=-1.748;CADD_phred=0.010;GERP++_RS=-3.61;phyloP46way_placental=-1.273;phyloP100way_vertebrate=-1.473;SiPhy_29way_logOdds=5.646;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|OR2L8|OR2L8|transcript|NM_001001963.1|protein_coding|1/1|c.635G>C|p.Gly212Ala|635/939|635/939|212/312||,C|intron_variant|MODIFIER|OR2L13|OR2L13|transcript|NM_001304535.1|protein_coding|1/1|c.-19+12108G>C||||||,C|intron_variant|MODIFIER|OR2L13|OR2L13|transcript|NM_175911.3|protein_coding|1/2|c.-144+12108G>C|||||| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:11:11,0:6,0:5,0:0.000 0/1:.:47:36,11:23,3:13,8:0.234 +chr2 43819994 rs200839584 C T . PASS DP=162;SOMATIC;SS=2;SSC=94;GPV=1;SPV=3.2187e-10;CLNACC=.,RCV000310689.2|RCV001143371.1;CLNDISDB=.,MedGen:CN517202|GeneReviews:NBK131810/MONDO:MONDO:0020747/MedGen:C5231390/OMIM:210250;CLNDN=.,not_provided|Sitosterolemia_1;CLNORIGIN=.,1;CLNREVSTAT=.,single|single;CLNSIG=.,0|0;CLNVI=.,Illumina_Clinical_Services_Laboratory\x2cIllumina:764360;FREQ=1000Genomes:0.9996,0.0003994|ExAC:0.9999,9.887e-05|GnomAD:1,4.28e-05|GnomAD_exomes:0.9999,0.0001074|PAGE_STUDY:0.9998,0.0001652|TOPMED:0.9999,6.8e-05|dbGaP_PopFreq:0.9999,7.061e-05;GENEINFO=DYNC2LI1:51626|ABCG5:64240;INT;NSM;R3;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.33;SIFT_pred=T;Polyphen2_HDIV_score=0.279;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.04;Polyphen2_HVAR_pred=B;LRT_score=0.078;LRT_pred=N;MutationTaster_score=0.997;MutationTaster_pred=N;MutationAssessor_score=1.375;MutationAssessor_pred=L;FATHMM_score=-0.63;FATHMM_pred=T;RadialSVM_score=-0.980;RadialSVM_pred=T;LR_score=0.189;LR_pred=T;VEST3_score=0.114;CADD_raw=-0.627;CADD_phred=1.219;GERP++_RS=-2.75;phyloP46way_placental=-0.921;phyloP100way_vertebrate=0.120;SiPhy_29way_logOdds=12.741;CLNALLELEID=268994;CLNDN=Sitosterolemia_1|not_provided;CLNDISDB=MONDO:MONDO:0020747,MedGen:C5231390,OMIM:210250|MedGen:CN517202;CLNREVSTAT=criteria_provided,_multiple_submitters,_no_conflicts;CLNSIG=Uncertain_significance;ALLELE_END;ANN=T|missense_variant|MODERATE|ABCG5|ABCG5|transcript|NM_022436.2|protein_coding|11/13|c.1570G>A|p.Val524Ile|1710/2740|1570/1956|524/651|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:48:48,0:27,0:21,0:0.000 0/1:.:114:64,50:32,33:32,17:0.439 +chr2 47805601 . AT A . MinMMQSdiff DP=126;SOMATIC;SS=2;SSC=16;GPV=1;SPV=0.025068;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=94891;CLNDN=Hereditary_nonpolyposis_colorectal_cancer_type_5|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided;CLNDISDB=MONDO:MONDO:0013710,MedGen:C1833477,OMIM:614350|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202;CLNREVSTAT=criteria_provided,_multiple_submitters,_no_conflicts;CLNSIG=Benign/Likely_benign;ALLELE_END;ANN=A|splice_region_variant&intron_variant|LOW|MSH6|MSH6|transcript|NM_000179.2|protein_coding|6/9|c.3557-4delT||||||INFO_REALIGN_3_PRIME,A|splice_region_variant&intron_variant|LOW|MSH6|MSH6|transcript|NM_001281492.1|protein_coding|4/7|c.3167-4delT||||||INFO_REALIGN_3_PRIME,A|splice_region_variant&intron_variant|LOW|MSH6|MSH6|transcript|NM_001281493.1|protein_coding|5/8|c.2651-4delT||||||INFO_REALIGN_3_PRIME,A|splice_region_variant&intron_variant|LOW|MSH6|MSH6|transcript|NM_001281494.1|protein_coding|6/9|c.2651-4delT||||||INFO_REALIGN_3_PRIME,A|downstream_gene_variant|MODIFIER|FBXO11|FBXO11|transcript|NM_001190274.1|protein_coding||c.*2516delA|||||1318|,A|downstream_gene_variant|MODIFIER|FBXO11|FBXO11|transcript|NM_025133.4|protein_coding||c.*2516delA|||||1318| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:35:33,0:19,0:14,0:0.000 0/1:.:91:77,11:44,6:33,5:0.125 +chr2 165953651 . G GCCCGCTCACCCGCTCA . MinMMQSdiff DP=49;SOMATIC;SS=2;SSC=17;GPV=1;SPV=0.018691;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=405364;CLNDN=not_specified;CLNDISDB=MedGen:CN169374;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Likely_benign;ALLELE_END;ANN=GCCCGCTCACCCGCTCA|upstream_gene_variant|MODIFIER|LOC102724058|LOC102724058|transcript|NR_110598.1|pseudogene||n.-3767_-3766insCCCGCTCACCCGCTCA|||||3766|,GCCCGCTCACCCGCTCA|intron_variant|MODIFIER|TTC21B|TTC21B|transcript|NM_024753.4|protein_coding|1/28|c.21+18_21+33dupTGAGCGGGTGAGCGGG|||||| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:11:6,1:5,0:1,1:0.143 0/1:.:38:7,15:5,6:2,9:0.682 +chr4 2898230 . T C . PASS DP=150;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.048075;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0;SIFT_pred=D;Polyphen2_HDIV_score=1.0;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=1.0;Polyphen2_HVAR_pred=D;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=1.75;MutationAssessor_pred=L;FATHMM_score=0.82;FATHMM_pred=T;RadialSVM_score=-0.555;RadialSVM_pred=T;LR_score=0.270;LR_pred=T;VEST3_score=0.978;CADD_raw=4.849;CADD_phred=27.6;GERP++_RS=5.86;phyloP46way_placental=2.235;phyloP100way_vertebrate=7.975;SiPhy_29way_logOdds=16.256;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|ADD1|ADD1|transcript|NM_014189.3|protein_coding|7/15|c.788T>C|p.Leu263Pro|976/4047|788/2307|263/768||,C|missense_variant|MODERATE|ADD1|ADD1|transcript|NM_001119.4|protein_coding|7/15|c.788T>C|p.Leu263Pro|976/3954|788/2214|263/737||,C|missense_variant|MODERATE|ADD1|ADD1|transcript|NM_014190.3|protein_coding|7/16|c.788T>C|p.Leu263Pro|976/3988|788/1896|263/631||,C|missense_variant|MODERATE|ADD1|ADD1|transcript|NM_176801.2|protein_coding|7/16|c.788T>C|p.Leu263Pro|976/4081|788/1989|263/662||,C|missense_variant|MODERATE|ADD1|ADD1|transcript|NM_001286645.1|protein_coding|8/18|c.788T>C|p.Leu263Pro|1651/4756|788/1989|263/662|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:52:51,0:20,0:31,0:0.000 0/1:.:98:90,7:25,6:65,1:0.072 +chr5 38476522 . C CT . PASS DP=153;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11056;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=297531;CLNDN=Stüve-Wiedemann_syndrome;CLNDISDB=MONDO:MONDO:0011108,MedGen:C0796176,OMIM:601559,Orphanet:ORPHA3206;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;ALLELE_END;ANN=CT|3_prime_UTR_variant|MODIFIER|LIFR|LIFR|transcript|NM_001127671.1|protein_coding|20/20|c.*5072dupA|||||5072|,CT|3_prime_UTR_variant|MODIFIER|LIFR|LIFR|transcript|NM_002310.5|protein_coding|20/20|c.*5072dupA|||||5072| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:48:45,0:22,0:23,0:0.000 0/1:.:105:98,6:60,3:38,3:0.058 +chr5 112775612 . TA T . PASS DP=161;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.042342;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=180169;CLNDN=Hereditary_cancer-predisposing_syndrome|not_specified|not_provided;CLNDISDB=MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202;CLNREVSTAT=criteria_provided,_multiple_submitters,_no_conflicts;CLNSIG=Benign/Likely_benign;ALLELE_END;ANN=T|splice_region_variant&intron_variant|LOW|APC|APC|transcript|NM_000038.5|protein_coding|4/15|c.423-4delA||||||INFO_REALIGN_3_PRIME,T|splice_region_variant&intron_variant|LOW|APC|APC|transcript|NM_001127511.2|protein_coding|3/13|c.453-4delA||||||INFO_REALIGN_3_PRIME,T|splice_region_variant&intron_variant|LOW|APC|APC|transcript|NM_001127510.2|protein_coding|5/16|c.423-4delA||||||INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:47:46,1:24,1:22,0:0.021 0/1:.:114:98,13:52,7:46,6:0.117 +chr5 141527699 . TA T . MinMMQSdiff DP=123;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.039946;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=501019;CLNDN=not_specified;CLNDISDB=MedGen:CN169374;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;ALLELE_END;ANN=T|splice_region_variant&intron_variant|LOW|DIAPH1|DIAPH1|transcript|NM_005219.4|protein_coding|23/27|c.3149-3delT||||||,T|splice_region_variant&intron_variant|LOW|DIAPH1|DIAPH1|transcript|NM_001079812.2|protein_coding|22/26|c.3122-3delT||||||,T|splice_region_variant&intron_variant|LOW|DIAPH1|DIAPH1|transcript|NM_001314007.1|protein_coding|23/28|c.3149-3delT|||||| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:34:22,1:12,1:10,0:0.043 0/1:.:89:59,17:31,7:28,10:0.224 +chr6 13364935 rs1407685850 A C . PASS DP=73;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.078592;FREQ=GnomAD:1,.,7.13e-06|TOMMO:0.9993,0.0006563,.|TOPMED:1,.,3.778e-06|dbGaP_PopFreq:0.9999,.,7.117e-05;GENEINFO=GFOD1:54438;NSM;R3;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=1;SIFT_pred=T;Polyphen2_HDIV_score=0.902;Polyphen2_HDIV_pred=P;Polyphen2_HVAR_score=0.468;Polyphen2_HVAR_pred=P;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=1.32;MutationAssessor_pred=L;FATHMM_score=1.6;FATHMM_pred=T;RadialSVM_score=-1.023;RadialSVM_pred=T;LR_score=0.037;LR_pred=T;VEST3_score=0.42;CADD_raw=2.989;CADD_phred=15.97;GERP++_RS=1.29;phyloP46way_placental=0.058;phyloP100way_vertebrate=-0.523;SiPhy_29way_logOdds=11.050;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|GFOD1|GFOD1|transcript|NM_018988.3|protein_coding|2/2|c.981T>G|p.Asp327Glu|1728/3308|981/1173|327/390||,C|missense_variant|MODERATE|GFOD1|GFOD1|transcript|NM_001242630.1|protein_coding|2/2|c.672T>G|p.Asp224Glu|956/2536|672/864|224/287||,C|missense_variant|MODERATE|GFOD1|GFOD1|transcript|NM_001242628.1|protein_coding|2/2|c.672T>G|p.Asp224Glu|901/2481|672/864|224/287|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:21:21,0:6,0:15,0:0.000 0/1:.:52:44,7:17,6:27,1:0.137 +chr6 47878370 rs746678221 C T . PASS DP=178;SOMATIC;SS=2;SSC=88;GPV=1;SPV=1.5004e-09;FREQ=ExAC:1,1.68e-05|GnomAD:1,1.428e-05|GnomAD_exomes:1,2.007e-05|TOPMED:1,1.889e-05|dbGaP_PopFreq:1,4.341e-05;GENEINFO=PTCHD4:442213;NSM;R3;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.57;SIFT_pred=T;Polyphen2_HDIV_score=0.105;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.005;Polyphen2_HVAR_pred=B;LRT_score=0.001;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=0;MutationAssessor_pred=N;FATHMM_score=-2.95;FATHMM_pred=D;RadialSVM_score=-0.486;RadialSVM_pred=T;LR_score=0.343;LR_pred=T;VEST3_score=0.375;CADD_raw=2.859;CADD_phred=15.52;GERP++_RS=5.29;phyloP46way_placental=1.612;phyloP100way_vertebrate=4.614;SiPhy_29way_logOdds=15.443;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=T|missense_variant|MODERATE|PTCHD4|PTCHD4|transcript|NM_001013732.3|protein_coding|3/3|c.2474G>A|p.Arg825Gln|2508/2850|2474/2541|825/846|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:46:46,0:18,0:28,0:0.000 0/1:.:132:77,55:38,30:39,25:0.417 +chr7 103149391 rs1813278496 T C . PASS DP=37;SOMATIC;SS=2;SSC=12;GPV=1;SPV=0.057896;FREQ=TOMMO:0.9981,0.00191;GENEINFO=NAPEPLD:222236|LOC105375434:105375434;INT;NSM;R5;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.82;SIFT_pred=T;Polyphen2_HDIV_score=0.0;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.0;Polyphen2_HVAR_pred=B;LRT_score=.;LRT_pred=.;MutationTaster_score=1.000;MutationTaster_pred=N;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=1.34;FATHMM_pred=T;RadialSVM_score=-0.990;RadialSVM_pred=T;LR_score=0.034;LR_pred=T;VEST3_score=0.019;CADD_raw=-0.828;CADD_phred=0.604;GERP++_RS=0.629;phyloP46way_placental=0.144;phyloP100way_vertebrate=-0.534;SiPhy_29way_logOdds=4.841;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|upstream_gene_variant|MODIFIER|NAPEPLD|NAPEPLD|transcript|NM_001122838.1|protein_coding||c.-20615A>G|||||269|,C|upstream_gene_variant|MODIFIER|NAPEPLD|NAPEPLD|transcript|NM_198990.4|protein_coding||c.-20615A>G|||||269|,C|intergenic_region|MODIFIER|NAPEPLD-DPY19L2P2|NAPEPLD-DPY19L2P2|intergenic_region|NAPEPLD-DPY19L2P2|||n.103149391T>C|||||| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:13:13,0:5,0:8,0:0.000 0/1:.:24:18,6:4,4:14,2:0.250 +chr7 107202971 . AT A . MinMMQSdiff DP=172;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.043842;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=301392;CLNDN=Congenital_disorder_of_glycosylation;CLNDISDB=MONDO:MONDO:0015286,MedGen:C0282577,OMIM:PS212065,Orphanet:ORPHA137,SNOMED_CT:238049009;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Likely_benign;ALLELE_END;ANN=A|3_prime_UTR_variant|MODIFIER|COG5|COG5|transcript|NM_006348.3|protein_coding|22/22|c.*544delA|||||544|,A|3_prime_UTR_variant|MODIFIER|COG5|COG5|transcript|NM_181733.2|protein_coding|21/21|c.*544delA|||||544|,A|downstream_gene_variant|MODIFIER|HBP1|HBP1|transcript|NM_001244262.1|protein_coding||c.*1541delT|||||443|,A|downstream_gene_variant|MODIFIER|HBP1|HBP1|transcript|NM_012257.3|protein_coding||c.*1541delT|||||443|,A|downstream_gene_variant|MODIFIER|COG5|COG5|transcript|NM_001161520.1|protein_coding||c.*7550delA|||||4881| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:38:37,1:27,0:10,1:0.026 0/1:.:134:107,17:60,13:47,4:0.137 +chr8 31076300 . CT C . MinMMQSdiff DP=172;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.087593;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=790795;CLNDN=Werner_syndrome;CLNDISDB=MONDO:MONDO:0010196,MedGen:C0043119,OMIM:277700,Orphanet:ORPHA902,SNOMED_CT:51626007;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;ALLELE_END;ANN=C|intron_variant|MODIFIER|WRN|WRN|transcript|NM_000553.4|protein_coding|8/34|c.839+25delT||||||INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:50:47,0:24,0:23,0:0.000 0/1:.:122:109,7:61,5:48,2:0.060 +chr8 80687384 rs1585953247 T C . PASS DP=63;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.094475;FREQ=Korea1K:1,0,.|TOPMED:1,.,3.778e-06|dbGaP_PopFreq:1,.,0;GENEINFO=ZNF704:619279;NSM;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.39;SIFT_pred=T;Polyphen2_HDIV_score=0.143;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.143;Polyphen2_HVAR_pred=B;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=2.08;MutationAssessor_pred=M;FATHMM_score=1.55;FATHMM_pred=T;RadialSVM_score=-1.053;RadialSVM_pred=T;LR_score=0.097;LR_pred=T;VEST3_score=0.34;CADD_raw=3.183;CADD_phred=16.65;GERP++_RS=5.7;phyloP46way_placental=2.173;phyloP100way_vertebrate=4.803;SiPhy_29way_logOdds=15.974;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|ZNF704|ZNF704|transcript|NM_001033723.2|protein_coding|4/9|c.400A>G|p.Ser134Gly|632/14386|400/1239|134/412|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:19:19,0:8,0:11,0:0.000 0/1:.:44:36,6:19,3:17,3:0.143 +chr9 85956346 . C CT . PASS DP=182;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10506;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=CT|splice_acceptor_variant&intron_variant|HIGH|NAA35|NAA35|transcript|NM_001321881.1|protein_coding|2/22|c.125-3dupT||||||INFO_REALIGN_3_PRIME,CT|splice_acceptor_variant&intron_variant|HIGH|NAA35|NAA35|transcript|NM_024635.3|protein_coding|2/22|c.125-3dupT||||||INFO_REALIGN_3_PRIME,CT|splice_acceptor_variant&intron_variant|HIGH|NAA35|NAA35|transcript|NM_001321882.1|protein_coding|2/22|c.125-3dupT||||||INFO_REALIGN_3_PRIME;LOF=(NAA35|NAA35|3|1.00) GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:56:54,0:38,0:16,0:0.000 0/1:.:126:115,6:67,5:48,1:0.050 +chr9 112574594 . C T . PASS DP=124;SOMATIC;SS=2;SSC=18;GPV=1;SPV=0.01311;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0;SIFT_pred=D;Polyphen2_HDIV_score=1.0;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.996;Polyphen2_HVAR_pred=D;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=0.695;MutationAssessor_pred=N;FATHMM_score=0.96;FATHMM_pred=T;RadialSVM_score=-0.785;RadialSVM_pred=T;LR_score=0.190;LR_pred=T;VEST3_score=0.829;CADD_raw=3.837;CADD_phred=19.49;GERP++_RS=6.07;phyloP46way_placental=2.884;phyloP100way_vertebrate=4.349;SiPhy_29way_logOdds=20.644;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=T|missense_variant|MODERATE|KIAA1958|KIAA1958|transcript|NM_001287036.1|protein_coding|2/5|c.514C>T|p.Arg172Cys|689/7652|514/2235|172/744||,T|missense_variant|MODERATE|KIAA1958|KIAA1958|transcript|NM_001287038.1|protein_coding|2/4|c.514C>T|p.Arg172Cys|689/7558|514/1347|172/448||,T|missense_variant|MODERATE|KIAA1958|KIAA1958|transcript|NM_133465.3|protein_coding|2/4|c.514C>T|p.Arg172Cys|689/7568|514/2151|172/716|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:42:42,0:13,0:29,0:0.000 0/1:.:82:72,10:39,4:33,6:0.122 +chr9 127651572 . CCT C . MinMMQSdiff DP=149;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10418;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=202275;CLNDN=not_specified;CLNDISDB=MedGen:CN169374;CLNREVSTAT=criteria_provided,_multiple_submitters,_no_conflicts;CLNSIG=Benign;ALLELE_END;ANN=C|intron_variant|MODIFIER|STXBP1|STXBP1|transcript|NM_003165.3|protein_coding|1/19|c.38-16_38-15delCT||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|STXBP1|STXBP1|transcript|NM_001032221.3|protein_coding|1/18|c.38-16_38-15delCT||||||INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:46:46,0:30,0:16,0:0.000 0/1:.:103:97,6:53,3:44,3:0.058 +chr9 130664691 . T C . PASS DP=51;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11761;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.04;SIFT_pred=D;Polyphen2_HDIV_score=0.009;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.005;Polyphen2_HVAR_pred=B;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=0.695;MutationAssessor_pred=N;FATHMM_score=2.56;FATHMM_pred=T;RadialSVM_score=-1.060;RadialSVM_pred=T;LR_score=0.022;LR_pred=T;VEST3_score=0.912;CADD_raw=2.439;CADD_phred=14.11;GERP++_RS=3.23;phyloP46way_placental=1.594;phyloP100way_vertebrate=7.058;SiPhy_29way_logOdds=8.170;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|PRDM12|PRDM12|transcript|NM_021619.2|protein_coding|1/5|c.38T>C|p.Leu13Pro|98/2492|38/1104|13/367|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:16:16,0:12,0:4,0:0.000 0/1:.:35:27,5:18,1:9,4:0.156 +chr10 87965536 . CT C . PASS DP=175;SOMATIC;SS=2;SSC=17;GPV=1;SPV=0.01923;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=240890;CLNDN=PTEN_hamartoma_tumor_syndrome;CLNDISDB=MONDO:MONDO:0017623,MedGen:C1959582,OMIM:601728,Orphanet:ORPHA306498;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;ALLELE_END;ANN=C|3_prime_UTR_variant|MODIFIER|PTEN|PTEN|transcript|NM_001304717.2|protein_coding|10/10|c.*75delT|||||75|INFO_REALIGN_3_PRIME,C|3_prime_UTR_variant|MODIFIER|PTEN|PTEN|transcript|NM_000314.6|protein_coding|9/9|c.*75delT|||||75|INFO_REALIGN_3_PRIME,C|3_prime_UTR_variant|MODIFIER|PTEN|PTEN|transcript|NM_001304718.1|protein_coding|9/9|c.*75delT|||||75|INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:55:54,0:30,0:24,0:0.000 0/1:.:120:106,10:66,9:40,1:0.086 +chr11 62786683 rs2084280733 T C . PASS DP=52;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.040211;FREQ=TOMMO:0.9989,0.001074;GENEINFO=TAF6L:10629|TMEM179B:374395;NSM;R5;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.09;SIFT_pred=T;Polyphen2_HDIV_score=0.0;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.001;Polyphen2_HVAR_pred=B;LRT_score=0.071;LRT_pred=N;MutationTaster_score=0.999;MutationTaster_pred=N;MutationAssessor_score=0.345;MutationAssessor_pred=N;FATHMM_score=0.88;FATHMM_pred=T;RadialSVM_score=-1.057;RadialSVM_pred=T;LR_score=0.051;LR_pred=T;VEST3_score=0.314;CADD_raw=0.607;CADD_phred=7.271;GERP++_RS=1.57;phyloP46way_placental=0.485;phyloP100way_vertebrate=1.378;SiPhy_29way_logOdds=4.335;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|TAF6L|TAF6L|transcript|NM_006473.3|protein_coding|11/11|c.1256T>C|p.Leu419Pro|1457/2115|1256/1869|419/622||,C|upstream_gene_variant|MODIFIER|TMEM179B|TMEM179B|transcript|NM_199337.2|protein_coding||c.-749T>C|||||719|,C|upstream_gene_variant|MODIFIER|MIR6748|MIR6748|transcript|NR_106806.1|pseudogene||n.-3132T>C|||||3132|,C|downstream_gene_variant|MODIFIER|TMEM223|TMEM223|transcript|NM_001080501.2|protein_coding||c.*3940A>G|||||3632| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:16:16,0:9,0:7,0:0.000 0/1:.:36:28,8:16,1:12,7:0.222 +chr12 52601418 . T C . PASS DP=87;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10996;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=1;SIFT_pred=T;Polyphen2_HDIV_score=0.212;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.055;Polyphen2_HVAR_pred=B;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=-0.46;MutationAssessor_pred=N;FATHMM_score=-1.52;FATHMM_pred=D;RadialSVM_score=-0.798;RadialSVM_pred=T;LR_score=0.191;LR_pred=T;VEST3_score=0.351;CADD_raw=0.738;CADD_phred=7.920;GERP++_RS=3.26;phyloP46way_placental=1.025;phyloP100way_vertebrate=-0.187;SiPhy_29way_logOdds=8.397;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|KRT72|KRT72|transcript|NM_001146225.1|protein_coding|1/10|c.35A>G|p.Glu12Gly|121/1888|35/1536|12/511||,C|missense_variant|MODERATE|KRT72|KRT72|transcript|NM_001146226.1|protein_coding|1/8|c.35A>G|p.Glu12Gly|121/1889|35/1410|12/469||,C|missense_variant|MODERATE|KRT72|KRT72|transcript|NM_080747.2|protein_coding|1/9|c.35A>G|p.Glu12Gly|121/2015|35/1536|12/511|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:26:26,0:17,0:9,0:0.000 0/1:.:61:55,6:40,5:15,1:0.098 +chr12 53467852 . TA T . PASS DP=136;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10327;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=ID\x3dCOSM1606323\x3bOCCURENCE\x3d1(liver);SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=T|downstream_gene_variant|MODIFIER|PCBP2-OT1|PCBP2-OT1|transcript|NR_109828.1|pseudogene||n.*2796delA|||||2796|,T|intron_variant|MODIFIER|PCBP2|PCBP2|transcript|NM_005016.5|protein_coding|12/14|c.838+22delA||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|PCBP2|PCBP2|transcript|NM_001098620.2|protein_coding|11/13|c.733+22delA||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|PCBP2|PCBP2|transcript|NM_001128911.1|protein_coding|12/14|c.838+22delA||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|PCBP2|PCBP2|transcript|NM_001128912.1|protein_coding|12/14|c.826+22delA||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|PCBP2|PCBP2|transcript|NM_001128913.1|protein_coding|11/13|c.745+22delA||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|PCBP2|PCBP2|transcript|NM_001128914.1|protein_coding|10/12|c.694+572delA||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|PCBP2|PCBP2|transcript|NM_031989.4|protein_coding|12/14|c.826+22delA||||||INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:38:36,0:18,0:18,0:0.000 0/1:.:98:90,7:39,3:51,4:0.072 +chr12 75207331 . A G . PASS DP=78;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10007;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0;SIFT_pred=D;Polyphen2_HDIV_score=1.0;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.993;Polyphen2_HVAR_pred=D;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=3.105;MutationAssessor_pred=M;FATHMM_score=-4.78;FATHMM_pred=D;RadialSVM_score=1.096;RadialSVM_pred=D;LR_score=0.966;LR_pred=D;VEST3_score=0.989;CADD_raw=4.158;CADD_phred=21.5;GERP++_RS=4.44;phyloP46way_placental=1.973;phyloP100way_vertebrate=8.932;SiPhy_29way_logOdds=14.145;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=G|missense_variant|MODERATE|KCNC2|KCNC2|transcript|NM_139137.3|protein_coding|2/5|c.653T>C|p.Leu218Pro|1214/5505|653/1917|218/638||,G|missense_variant|MODERATE|KCNC2|KCNC2|transcript|NM_001260497.1|protein_coding|2/5|c.653T>C|p.Leu218Pro|1214/6077|653/1857|218/618||,G|missense_variant|MODERATE|KCNC2|KCNC2|transcript|NM_001260498.1|protein_coding|2/5|c.653T>C|p.Leu218Pro|1214/3470|653/1890|218/629||,G|missense_variant|MODERATE|KCNC2|KCNC2|transcript|NM_001260499.1|protein_coding|2/4|c.653T>C|p.Leu218Pro|1214/5340|653/1752|218/583||,G|missense_variant|MODERATE|KCNC2|KCNC2|transcript|NM_139136.3|protein_coding|2/6|c.653T>C|p.Leu218Pro|1214/3565|653/1842|218/613||,G|missense_variant|MODERATE|KCNC2|KCNC2|transcript|NM_153748.2|protein_coding|2/5|c.653T>C|p.Leu218Pro|1214/3400|653/1677|218/558|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:21:21,0:9,0:12,0:0.000 0/1:.:57:50,7:20,4:30,3:0.123 +chr12 109999777 rs1889849841 A G . PASS DP=67;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.099397;FREQ=TOMMO:0.9961,0.003878;GENEINFO=ANKRD13A:88455;INT;NSM;SSR=0;U5;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=1;SIFT_pred=T;Polyphen2_HDIV_score=0.0;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.001;Polyphen2_HVAR_pred=B;LRT_score=0.090;LRT_pred=N;MutationTaster_score=0.835;MutationTaster_pred=D;MutationAssessor_score=0.315;MutationAssessor_pred=N;FATHMM_score=-0.11;FATHMM_pred=T;RadialSVM_score=-0.977;RadialSVM_pred=T;LR_score=0.089;LR_pred=T;VEST3_score=0.07;CADD_raw=0.273;CADD_phred=5.475;GERP++_RS=1.08;phyloP46way_placental=0.419;phyloP100way_vertebrate=0.106;SiPhy_29way_logOdds=7.367;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=G|missense_variant|MODERATE|ANKRD13A|ANKRD13A|transcript|NM_033121.1|protein_coding|1/15|c.89A>G|p.Gln30Arg|348/3908|89/1773|30/590||,G|upstream_gene_variant|MODIFIER|GIT2|GIT2|transcript|NM_057169.4|protein_coding||c.-3553T>C|||||3388|,G|upstream_gene_variant|MODIFIER|GIT2|GIT2|transcript|NM_001135213.2|protein_coding||c.-3553T>C|||||3388|,G|upstream_gene_variant|MODIFIER|GIT2|GIT2|transcript|NM_001135214.2|protein_coding||c.-3553T>C|||||3388|,G|upstream_gene_variant|MODIFIER|GIT2|GIT2|transcript|NM_001330153.1|protein_coding||c.-3553T>C|||||3388|,G|upstream_gene_variant|MODIFIER|GIT2|GIT2|transcript|NM_014776.4|protein_coding||c.-3553T>C|||||3388|,G|upstream_gene_variant|MODIFIER|GIT2|GIT2|transcript|NM_057170.4|protein_coding||c.-3553T>C|||||3388|,G|upstream_gene_variant|MODIFIER|GIT2|GIT2|transcript|NM_001330154.1|protein_coding||c.-3553T>C|||||3388|,G|upstream_gene_variant|MODIFIER|GIT2|GIT2|transcript|NM_139201.2|protein_coding||c.-3553T>C|||||3388| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:14:14,0:12,0:2,0:0.000 0/1:.:53:43,9:37,1:6,8:0.173 +chr13 36845100 . ATGTG A . MinMMQSdiff DP=122;SOMATIC;SS=2;SSC=14;GPV=1;SPV=0.036896;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=336095;CLNDN=Primary_pulmonary_hypertension_1;CLNDISDB=MONDO:MONDO:0024533,MedGen:C4552070,OMIM:178600;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;ALLELE_END;ANN=A|3_prime_UTR_variant|MODIFIER|SMAD9|SMAD9|transcript|NM_001127217.2|protein_coding|7/7|c.*3572_*3575delCACA|||||3572|,A|3_prime_UTR_variant|MODIFIER|SMAD9|SMAD9|transcript|NM_005905.5|protein_coding|6/6|c.*3572_*3575delCACA|||||3572| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:33:33,0:16,0:17,0:0.000 0/1:.:89:79,10:42,9:37,1:0.112 +chr14 53055920 . T TA . MinMMQSdiff DP=180;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.070254;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=685399;CLNDN=Spastic_paraplegia_28,_autosomal_recessive;CLNDISDB=MONDO:MONDO:0012256,MedGen:C1836295,OMIM:609340,Orphanet:ORPHA101008;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;ALLELE_END;ANN=TA|intron_variant|MODIFIER|DDHD1|DDHD1|transcript|NM_001160148.1|protein_coding|9/12|c.1993-9dupT||||||,TA|intron_variant|MODIFIER|DDHD1|DDHD1|transcript|NM_001160147.1|protein_coding|10/12|c.2014-9dupT||||||,TA|intron_variant|MODIFIER|DDHD1|DDHD1|transcript|NM_030637.2|protein_coding|9/11|c.1993-9dupT|||||| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:49:49,0:29,0:20,0:0.000 0/1:.:131:120,8:60,2:60,6:0.062 +chr14 60282825 . C T . PASS DP=137;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10575;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.02;SIFT_pred=D;Polyphen2_HDIV_score=0.984;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.564;Polyphen2_HVAR_pred=P;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=2.18;MutationAssessor_pred=M;FATHMM_score=2.25;FATHMM_pred=T;RadialSVM_score=-1.090;RadialSVM_pred=T;LR_score=0.081;LR_pred=T;VEST3_score=0.891;CADD_raw=4.216;CADD_phred=21.9;GERP++_RS=5.75;phyloP46way_placental=2.704;phyloP100way_vertebrate=7.818;SiPhy_29way_logOdds=19.923;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=T|structural_interaction_variant|HIGH|PPM1A|PPM1A|interaction|1A6Q:A_41-A_72:NM_021003.4|protein_coding|2/6|c.122C>T||||||,T|structural_interaction_variant|HIGH|PPM1A|PPM1A|interaction|3FXJ:A_41-A_72:NM_021003.4|protein_coding|2/6|c.122C>T||||||,T|structural_interaction_variant|HIGH|PPM1A|PPM1A|interaction|3FXK:A_41-A_72:NM_021003.4|protein_coding|2/6|c.122C>T||||||,T|structural_interaction_variant|HIGH|PPM1A|PPM1A|interaction|3FXL:A_41-A_72:NM_021003.4|protein_coding|2/6|c.122C>T||||||,T|structural_interaction_variant|HIGH|PPM1A|PPM1A|interaction|3FXM:A_41-A_72:NM_021003.4|protein_coding|2/6|c.122C>T||||||,T|structural_interaction_variant|HIGH|PPM1A|PPM1A|interaction|3FXO:A_41-A_72:NM_021003.4|protein_coding|2/6|c.122C>T||||||,T|structural_interaction_variant|HIGH|PPM1A|PPM1A|interaction|4RA2:A_41-A_72:NM_021003.4|protein_coding|2/6|c.122C>T||||||,T|missense_variant|MODERATE|PPM1A|PPM1A|transcript|NM_177952.2|protein_coding|2/6|c.341C>T|p.Thr114Met|437/8069|341/1368|114/455||,T|missense_variant|MODERATE|PPM1A|PPM1A|transcript|NM_177951.2|protein_coding|3/4|c.122C>T|p.Thr41Met|674/4317|122/975|41/324||,T|missense_variant|MODERATE|PPM1A|PPM1A|transcript|NM_021003.4|protein_coding|2/6|c.122C>T|p.Thr41Met|572/8204|122/1149|41/382|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:42:42,0:18,0:24,0:0.000 0/1:.:95:89,6:39,4:50,2:0.063 +chr14 73064954 . C CT . MinMMQSdiff DP=141;SOMATIC;SS=2;SSC=20;GPV=1;SPV=0.0082366;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=794309;CLNDN=CIC-DUX_Sarcoma;CLNDISDB=MedGen:C3899764;CLNREVSTAT=no_assertion_provided;CLNSIG=not_provided;ALLELE_END;ANN=CT|intron_variant|MODIFIER|RBM25|RBM25|transcript|NM_021239.2|protein_coding|1/18|c.-16+6264dupT||||||INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:47:41,0:23,0:18,0:0.000 0/1:.:94:77,12:40,4:37,8:0.135 +chr14 95535217 . A G . PASS DP=25;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.093333;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.03;SIFT_pred=D;Polyphen2_HDIV_score=0.09;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.009;Polyphen2_HVAR_pred=B;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=2.94;MutationAssessor_pred=M;FATHMM_score=1.25;FATHMM_pred=T;RadialSVM_score=-0.923;RadialSVM_pred=T;LR_score=0.126;LR_pred=T;VEST3_score=0.231;CADD_raw=3.581;CADD_phred=18.24;GERP++_RS=3.55;phyloP46way_placental=0.813;phyloP100way_vertebrate=3.504;SiPhy_29way_logOdds=10.604;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=G|missense_variant|MODERATE|GLRX5|GLRX5|transcript|NM_016417.2|protein_coding|1/2|c.128A>G|p.Glu43Gly|232/1171|128/474|43/157||,G|upstream_gene_variant|MODIFIER|SNHG10|SNHG10|transcript|NR_003138.3|pseudogene||n.-345T>C|||||345|,G|upstream_gene_variant|MODIFIER|SCARNA13|SCARNA13|transcript|NR_003002.1|pseudogene||n.-1588T>C|||||1588|,G|upstream_gene_variant|MODIFIER|SNHG10|SNHG10|transcript|NR_001459.2|pseudogene||n.-345T>C|||||345| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:17:17,0:2,0:15,0:0.000 0/1:.:8:6,2:6,2:0,0:0.250 +chr14 104939447 . T C . PASS DP=137;SOMATIC;SS=2;SSC=42;GPV=1;SPV=5.4204e-05;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.38;SIFT_pred=T;Polyphen2_HDIV_score=0.0;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.001;Polyphen2_HVAR_pred=B;LRT_score=0.002;LRT_pred=U;MutationTaster_score=1.000;MutationTaster_pred=N;MutationAssessor_score=-0.345;MutationAssessor_pred=N;FATHMM_score=6.06;FATHMM_pred=T;RadialSVM_score=-0.921;RadialSVM_pred=T;LR_score=0.005;LR_pred=T;VEST3_score=0.032;CADD_raw=-0.972;CADD_phred=0.304;GERP++_RS=-4.01;phyloP46way_placental=-0.747;phyloP100way_vertebrate=-1.890;SiPhy_29way_logOdds=7.542;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|AHNAK2|AHNAK2|transcript|NM_138420.2|protein_coding|7/7|c.16004A>G|p.His5335Arg|16124/18317|16004/17388|5335/5795|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:30:30,0:18,0:12,0:0.000 0/1:.:107:73,34:35,17:38,17:0.318 +chr16 72788664 . T TTGC . MinMMQSdiff DP=85;SOMATIC;SS=2;SSC=16;GPV=1;SPV=0.020937;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=ID\x3dCOSM1379701\x3bOCCURENCE\x3d1(large_intestine);SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=TTGC|disruptive_inframe_insertion|MODERATE|ZFHX3|ZFHX3|transcript|NM_006885.3|protein_coding|10/10|c.9609_9611dupGCA|p.Gln3204dup|10284/16062|9611/11112|3204/3703||,TTGC|disruptive_inframe_insertion|MODERATE|ZFHX3|ZFHX3|transcript|NM_001164766.1|protein_coding|9/9|c.6867_6869dupGCA|p.Gln2290dup|6998/12776|6869/8370|2290/2789|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:21:19,2:7,2:12,0:0.095 0/1:.:64:39,21:19,12:20,9:0.350 +chr17 44248849 . G GT . MinMMQSdiff DP=41;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10791;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=344704;CLNDN=Hemolytic_anemia|Distal_Renal_Tubular_Acidosis,_Dominant|Spherocytosis,_Dominant;CLNDISDB=Human_Phenotype_Ontology:HP:0001878,Human_Phenotype_Ontology:HP:0001910,Human_Phenotype_Ontology:HP:0004827,Human_Phenotype_Ontology:HP:0004853,Human_Phenotype_Ontology:HP:0004868,Human_Phenotype_Ontology:HP:0005503,MONDO:MONDO:0003664,MedGen:C0002878|MedGen:CN239155|MedGen:CN239455;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Uncertain_significance;ALLELE_END;ANN=GT|3_prime_UTR_variant|MODIFIER|SLC4A1|SLC4A1|transcript|NM_000342.3|protein_coding|20/20|c.*1608dupA|||||1608| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:15:10,0:7,0:3,0:0.000 0/1:.:26:11,4:3,2:8,2:0.267 +chr17 76736877 rs751713049 G T . PASS DP=41;SOMATIC;SS=2;SSC=16;GPV=1;SPV=0.021382;CLNACC=.,.,RCV001293765.1,.;CLNDISDB=.,.,MONDO:MONDO:0020526/MedGen:CN207426,.;CLNDN=.,.,Acute_megakaryoblastic_leukemia_in_down_syndrome,.;CLNORIGIN=.,.,2,.;CLNREVSTAT=.,.,single,.;CLNSIG=.,.,4,.;FREQ=Korea1K:0.9994,0.0005593,.,.|TOMMO:0.9998,.,.,0.0002388|dbGaP_PopFreq:1,0,0,0;GENEINFO=SRSF2:6427|MFSD11:79157|MIR636:693221;NSM;R5;SSR=0;U5;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=ID\x3dCOSM211029,COSM211505,COSM211504\x3bOCCURENCE\x3d80(haematopoietic_and_lymphoid_tissue);SIFT_score=0.02;SIFT_pred=D;Polyphen2_HDIV_score=1.0;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.984;Polyphen2_HVAR_pred=D;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=2.56;MutationAssessor_pred=M;FATHMM_score=-0.94;FATHMM_pred=T;RadialSVM_score=-0.044;RadialSVM_pred=T;LR_score=0.532;LR_pred=D;VEST3_score=0.311;CADD_raw=2.169;CADD_phred=13.21;GERP++_RS=2.76;phyloP46way_placental=0.413;phyloP100way_vertebrate=8.573;SiPhy_29way_logOdds=8.660;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=T|missense_variant|MODERATE|SRSF2|SRSF2|transcript|NM_001195427.1|protein_coding|1/3|c.284C>A|p.Pro95His|535/1968|284/666|95/221||,T|missense_variant|MODERATE|SRSF2|SRSF2|transcript|NM_003016.4|protein_coding|1/2|c.284C>A|p.Pro95His|535/2963|284/666|95/221||,T|5_prime_UTR_variant|MODIFIER|MFSD11|MFSD11|transcript|NM_001242534.1|protein_coding|1/14|c.-286G>T|||||1476|,T|upstream_gene_variant|MODIFIER|MIR636|MIR636|transcript|NR_030366.1|pseudogene||n.-329C>A|||||329|,T|upstream_gene_variant|MODIFIER|MFSD11|MFSD11|transcript|NM_001242532.1|protein_coding||c.-1476G>T|||||624|,T|upstream_gene_variant|MODIFIER|MFSD11|MFSD11|transcript|NM_001242533.1|protein_coding||c.-1476G>T|||||624|,T|upstream_gene_variant|MODIFIER|MFSD11|MFSD11|transcript|NM_001242535.1|protein_coding||c.-1476G>T|||||624|,T|upstream_gene_variant|MODIFIER|MFSD11|MFSD11|transcript|NM_001242536.1|protein_coding||c.-1476G>T|||||624|,T|upstream_gene_variant|MODIFIER|MFSD11|MFSD11|transcript|NM_001242537.1|protein_coding||c.-1476G>T|||||624|,T|upstream_gene_variant|MODIFIER|MFSD11|MFSD11|transcript|NM_024311.3|protein_coding||c.-1476G>T|||||624|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001080510.4|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001206983.2|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001206984.2|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001206985.2|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001206986.2|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001206987.2|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001302703.1|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001302704.1|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001302705.1|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NR_038193.2|pseudogene||n.*2996G>T|||||2996|,T|non_coding_transcript_exon_variant|MODIFIER|SRSF2|SRSF2|transcript|NR_036608.1|pseudogene|1/4|n.535C>A|||||| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:16:16,0:10,0:6,0:0.000 0/1:.:25:18,7:14,2:4,5:0.280 +chr19 1065393 . G T . PASS DP=119;SOMATIC;SS=2;SSC=64;GPV=1;SPV=3.6034e-07;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.03;SIFT_pred=D;Polyphen2_HDIV_score=0.979;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.511;Polyphen2_HVAR_pred=P;LRT_score=.;LRT_pred=.;MutationTaster_score=1.000;MutationTaster_pred=N;MutationAssessor_score=0;MutationAssessor_pred=N;FATHMM_score=-2.22;FATHMM_pred=D;RadialSVM_score=-0.593;RadialSVM_pred=T;LR_score=0.375;LR_pred=T;VEST3_score=0.486;CADD_raw=2.144;CADD_phred=13.13;GERP++_RS=1.46;phyloP46way_placental=0.760;phyloP100way_vertebrate=0.687;SiPhy_29way_logOdds=5.290;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=T|missense_variant|MODERATE|ABCA7|ABCA7|transcript|NM_019112.3|protein_coding|47/47|c.6409G>T|p.Asp2137Tyr|6640/6818|6409/6441|2137/2146||,T|upstream_gene_variant|MODIFIER|ARHGAP45|ARHGAP45|transcript|NM_001258328.2|protein_coding||c.-633G>T|||||530|,T|upstream_gene_variant|MODIFIER|ARHGAP45|ARHGAP45|transcript|NM_012292.4|protein_coding||c.-2013G>T|||||1773|,T|upstream_gene_variant|MODIFIER|ARHGAP45|ARHGAP45|transcript|NM_001321232.1|protein_coding||c.-2180G>T|||||2105| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:32:32,0:21,0:11,0:0.000 0/1:.:87:49,38:31,30:18,8:0.437 +chr19 10467500 . A G . PASS DP=74;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11838;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.48;SIFT_pred=T;Polyphen2_HDIV_score=0.001;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.004;Polyphen2_HVAR_pred=B;LRT_score=0.000;LRT_pred=N;MutationTaster_score=0.958;MutationTaster_pred=N;MutationAssessor_score=0;MutationAssessor_pred=N;FATHMM_score=0.21;FATHMM_pred=T;RadialSVM_score=-1.029;RadialSVM_pred=T;LR_score=0.109;LR_pred=T;VEST3_score=0.042;CADD_raw=0.477;CADD_phred=6.589;GERP++_RS=-0.855;phyloP46way_placental=0.043;phyloP100way_vertebrate=0.494;SiPhy_29way_logOdds=6.149;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=G|missense_variant|MODERATE|PDE4A|PDE4A|transcript|NM_001111307.1|protein_coding|15/15|c.2540A>G|p.Glu847Gly|2648/4779|2540/2661|847/886||,G|missense_variant|MODERATE|PDE4A|PDE4A|transcript|NM_001243121.1|protein_coding|17/17|c.2474A>G|p.Glu825Gly|2558/4689|2474/2595|825/864||,G|missense_variant|MODERATE|PDE4A|PDE4A|transcript|NM_001111308.1|protein_coding|15/15|c.2462A>G|p.Glu821Gly|2462/4593|2462/2583|821/860||,G|missense_variant|MODERATE|PDE4A|PDE4A|transcript|NM_001111309.1|protein_coding|15/15|c.2357A>G|p.Glu786Gly|2357/4488|2357/2478|786/825||,G|missense_variant|MODERATE|PDE4A|PDE4A|transcript|NM_006202.2|protein_coding|10/10|c.1823A>G|p.Glu608Gly|2130/4261|1823/1944|608/647|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:25:25,0:6,0:19,0:0.000 0/1:.:49:44,5:18,4:26,1:0.102 +chr19 12721349 rs1966929781 A G . PASS DP=48;SOMATIC;SS=2;SSC=17;GPV=1;SPV=0.018465;FREQ=TOMMO:0.9993,0.0006567;GENEINFO=TNPO2:30000;INT;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=0.992;MutationTaster_pred=N;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=-1.032;RadialSVM_pred=T;LR_score=0.082;LR_pred=T;VEST3_score=.;CADD_raw=1.556;CADD_phred=11.16;GERP++_RS=2.16;phyloP46way_placental=1.245;phyloP100way_vertebrate=-0.288;SiPhy_29way_logOdds=6.333;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=G|intron_variant|MODIFIER|TNPO2|TNPO2|transcript|NM_001136196.1|protein_coding|1/24|c.-13-359T>C||||||,G|intron_variant|MODIFIER|TNPO2|TNPO2|transcript|NM_013433.4|protein_coding|1/24|c.-13-359T>C||||||,G|intron_variant|MODIFIER|TNPO2|TNPO2|transcript|NM_001136195.1|protein_coding|2/25|c.-13-359T>C|||||| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:13:13,0:8,0:5,0:0.000 0/1:.:35:24,11:15,8:9,3:0.314 +chr19 45795880 . T TCTCCTCGCCCTCCTCCTC . MinMMQSdiff DP=102;SOMATIC;SS=2;SSC=19;GPV=1;SPV=0.010588;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=ID\x3dCOSM253920\x3bOCCURENCE\x3d1(urinary_tract);SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=TCTCCTCGCCCTCCTCCTC|conservative_inframe_insertion|MODERATE|RSPH6A|RSPH6A|transcript|NM_030785.3|protein_coding|6/6|c.2125_2142dupGAGGAGGAGGGCGAGGAG|p.Glu714_Thr715insGluGluGluGlyGluGlu|2313/2484|2142/2154|714/717||,TCTCCTCGCCCTCCTCCTC|upstream_gene_variant|MODIFIER|DMWD|DMWD|transcript|NM_004943.1|protein_coding||c.-3142_-3125dupGAGGAGGAGGGCGAGGAG|||||3079| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:25:24,0:12,0:12,0:0.000 0/1:.:77:60,15:36,8:24,7:0.200 +chr20 6075049 . G GT . PASS DP=149;SOMATIC;SS=2;SSC=14;GPV=1;SPV=0.037662;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=351325;CLNDN=Kindler_syndrome;CLNDISDB=MONDO:MONDO:0008260,MedGen:C0406557,OMIM:173650,Orphanet:ORPHA2908,SNOMED_CT:238835001,SNOMED_CT:238836000;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Uncertain_significance;ALLELE_END;ANN=GT|3_prime_UTR_variant|MODIFIER|FERMT1|FERMT1|transcript|NM_017671.4|protein_coding|15/15|c.*2123dupA|||||2123| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:47:45,1:22,0:23,1:0.022 0/1:.:102:84,12:37,5:47,7:0.125 +chr20 32808191 . CT C . MinMMQSdiff DP=137;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10114;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=345075;CLNDN=Immunodeficiency-centromeric_instability-facial_anomalies_syndrome_1;CLNDISDB=MONDO:MONDO:0009454,MedGen:C4551557,OMIM:242860;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Uncertain_significance;ALLELE_END;ANN=C|3_prime_UTR_variant|MODIFIER|DNMT3B|DNMT3B|transcript|NM_006892.3|protein_coding|23/23|c.*299delT|||||299|INFO_REALIGN_3_PRIME,C|3_prime_UTR_variant|MODIFIER|DNMT3B|DNMT3B|transcript|NM_001207055.1|protein_coding|19/19|c.*299delT|||||299|INFO_REALIGN_3_PRIME,C|3_prime_UTR_variant|MODIFIER|DNMT3B|DNMT3B|transcript|NM_001207056.1|protein_coding|18/18|c.*299delT|||||299|INFO_REALIGN_3_PRIME,C|3_prime_UTR_variant|MODIFIER|DNMT3B|DNMT3B|transcript|NM_175848.1|protein_coding|22/22|c.*299delT|||||299|INFO_REALIGN_3_PRIME,C|3_prime_UTR_variant|MODIFIER|DNMT3B|DNMT3B|transcript|NM_175849.1|protein_coding|20/20|c.*299delT|||||299|INFO_REALIGN_3_PRIME,C|3_prime_UTR_variant|MODIFIER|DNMT3B|DNMT3B|transcript|NM_175850.2|protein_coding|22/22|c.*299delT|||||299|INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:37:36,0:21,0:15,0:0.000 0/1:.:100:89,7:46,5:43,2:0.073 +chr20 38836101 . G C . PASS DP=82;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.089735;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=1;SIFT_pred=T;Polyphen2_HDIV_score=0.018;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.02;Polyphen2_HVAR_pred=B;LRT_score=0.175;LRT_pred=N;MutationTaster_score=1.000;MutationTaster_pred=N;MutationAssessor_score=0.105;MutationAssessor_pred=N;FATHMM_score=-0.21;FATHMM_pred=T;RadialSVM_score=-0.989;RadialSVM_pred=T;LR_score=0.100;LR_pred=T;VEST3_score=0.167;CADD_raw=-1.674;CADD_phred=0.012;GERP++_RS=3.46;phyloP46way_placental=1.288;phyloP100way_vertebrate=1.830;SiPhy_29way_logOdds=4.802;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|PPP1R16B|PPP1R16B|transcript|NM_015568.3|protein_coding|2/11|c.176G>C|p.Gly59Ala|377/6263|176/1704|59/567||,C|missense_variant|MODERATE|PPP1R16B|PPP1R16B|transcript|NM_001172735.2|protein_coding|2/10|c.176G>C|p.Gly59Ala|377/6137|176/1578|59/525|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:23:23,0:14,0:9,0:0.000 0/1:.:59:52,7:41,1:11,6:0.119 +chr20 63307547 rs759710143 A G . PASS DP=90;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.074052;FREQ=ExAC:1,8.47e-06|GnomAD_exomes:1,4.036e-06|TOPMED:1,3.778e-06|dbGaP_PopFreq:1,0;GENEINFO=COL20A1:57642;NSM;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0;SIFT_pred=D;Polyphen2_HDIV_score=1.0;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.999;Polyphen2_HVAR_pred=D;LRT_score=0.000;LRT_pred=U;MutationTaster_score=0.999;MutationTaster_pred=D;MutationAssessor_score=4.565;MutationAssessor_pred=H;FATHMM_score=-4.64;FATHMM_pred=D;RadialSVM_score=1.047;RadialSVM_pred=D;LR_score=0.974;LR_pred=D;VEST3_score=0.769;CADD_raw=4.119;CADD_phred=21.2;GERP++_RS=3.92;phyloP46way_placental=1.418;phyloP100way_vertebrate=6.103;SiPhy_29way_logOdds=11.020;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=G|missense_variant|MODERATE|COL20A1|COL20A1|transcript|NM_020882.2|protein_coding|6/36|c.554A>G|p.Asp185Gly|654/4172|554/3855|185/1284|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:27:27,0:11,0:16,0:0.000 0/1:.:63:56,7:26,6:30,1:0.111 +chr21 32361892 rs371227097 C T . PASS DP=118;SOMATIC;SS=2;SSC=45;GPV=1;SPV=3.1599e-05;FREQ=1000Genomes:0.9998,0.0001997|ALSPAC:1,0|ExAC:1,4.72e-05|GnomAD:0.9998,0.0001711|GnomAD_exomes:0.9998,0.0002368|GoESP:0.9998,0.000219|MGP:0.9981,0.001873|TOPMED:0.9998,0.0002116|TWINSUK:0.9992,0.0008091|dbGaP_PopFreq:0.9998,0.0002345;GENEINFO=URB1:9875;NSM;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=1.0;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.926;Polyphen2_HVAR_pred=D;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=2.045;MutationAssessor_pred=M;FATHMM_score=1.49;FATHMM_pred=T;RadialSVM_score=-0.911;RadialSVM_pred=T;LR_score=0.169;LR_pred=T;VEST3_score=0.087;CADD_raw=3.753;CADD_phred=19.05;GERP++_RS=5.26;phyloP46way_placental=2.608;phyloP100way_vertebrate=1.875;SiPhy_29way_logOdds=15.945;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=T|missense_variant&splice_region_variant|MODERATE|URB1|URB1|transcript|NM_014825.2|protein_coding|12/39|c.1639G>A|p.Asp547Asn|1732/10808|1639/6816|547/2271|| GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:31:31,0:14,0:17,0:0.000 0/1:.:87:58,29:31,16:27,13:0.333
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/computed_VAFs_2.vcf Mon Nov 28 21:59:34 2022 +0000 @@ -0,0 +1,248 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=PASS,Description="All filters passed"> +##reference=/home/galaxy/galaxy/tool-data/hg38-bgi-light/sam_indexes/hg38-bgi-light/hg38-bgi-light.fa +##source=varscan.py +##contig=<ID=chr1,length=248956422> +##contig=<ID=chr10,length=133797422> +##contig=<ID=chr11,length=135086622> +##contig=<ID=chr12,length=133275309> +##contig=<ID=chr13,length=114364328> +##contig=<ID=chr14,length=107043718> +##contig=<ID=chr15,length=101991189> +##contig=<ID=chr16,length=90338345> +##contig=<ID=chr17,length=83257441> +##contig=<ID=chr18,length=80373285> +##contig=<ID=chr19,length=58617616> +##contig=<ID=chr2,length=242193529> +##contig=<ID=chr20,length=64444167> +##contig=<ID=chr21,length=46709983> +##contig=<ID=chr22,length=50818468> +##contig=<ID=chr3,length=198295559> +##contig=<ID=chr4,length=190214555> +##contig=<ID=chr5,length=181538259> +##contig=<ID=chr6,length=170805979> +##contig=<ID=chr7,length=159345973> +##contig=<ID=chr8,length=145138636> +##contig=<ID=chr9,length=138394717> +##contig=<ID=chrM,length=16569> +##contig=<ID=chrX,length=156040895> +##contig=<ID=chrY,length=57227415> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases"> +##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation"> +##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)"> +##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value"> +##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls"> +##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls"> +##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand"> +##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position"> +##FILTER=<ID=VarCount,Description="Fewer than 4 variant-supporting reads"> +##FILTER=<ID=VarFreq,Description="Variant allele frequency below 0.05"> +##FILTER=<ID=VarAvgRL,Description="Average clipped length of variant-supporting reads < 90"> +##FILTER=<ID=VarReadPos,Description="Relative average read position < 0.1"> +##FILTER=<ID=VarDist3,Description="Average distance to effective 3' end < 0.1"> +##FILTER=<ID=VarMMQS,Description="Average mismatch quality sum for variant reads > 100"> +##FILTER=<ID=VarMapQual,Description="Average mapping quality of variant reads < 15"> +##FILTER=<ID=VarBaseQual,Description="Average base quality of variant reads < 15"> +##FILTER=<ID=Strand,Description="Strand representation of variant reads < 0.01"> +##FILTER=<ID=RefAvgRL,Description="Average clipped length of ref-supporting reads < 90"> +##FILTER=<ID=RefReadPos,Description="Relative average read position < 0.1"> +##FILTER=<ID=RefDist3,Description="Average distance to effective 3' end < 0.1"> +##FILTER=<ID=RefMapQual,Description="Average mapping quality of reference reads < 15"> +##FILTER=<ID=RefBaseQual,Description="Average base quality of ref-supporting reads < 15"> +##FILTER=<ID=RefMMQS,Description="Average mismatch quality sum for ref-supporting reads > 100"> +##FILTER=<ID=MMQSdiff,Description="Mismatch quality sum difference (var - ref) > 50"> +##FILTER=<ID=MinMMQSdiff,Description="Mismatch quality sum difference (var - ref) < 50"> +##FILTER=<ID=MapQualDiff,Description="Mapping quality difference (ref - var) > 50"> +##FILTER=<ID=MaxBAQdiff,Description="Average base quality difference (ref - var) > 50"> +##FILTER=<ID=ReadLenDiff,Description="Average supporting read length difference (ref - var) > 0.25"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype code"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth"> +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele"> +##FORMAT=<ID=ADF,Number=R,Type=Integer,Description="Read depth for each allele on the forward strand"> +##FORMAT=<ID=ADR,Number=R,Type=Integer,Description="Read depth for each allele on the reverse strand"> +##bcftools_filterVersion=1.10.2+htslib-1.10.2 +##bcftools_filterCommand=filter --include 'INFO/SPV < 0.12 | INFO/GPV < 0.12' --output-type v --threads 1 input.vcf.gz; Date=Thu Apr 21 00:52:51 2022 +##bcftools_concatVersion=1.10.2+htslib-1.10.2 +##bcftools_concatCommand=concat --allow-overlaps --min-PQ 30 --output-type v --threads 1 input0.vcf.gz input1.vcf.gz input2.vcf.gz input3.vcf.gz input4.vcf.gz input5.vcf.gz input6.vcf.gz input7.vcf.gz input8.vcf.gz input9.vcf.gz input10.vcf.gz input11.vcf.gz input12.vcf.gz input13.vcf.gz input14.vcf.gz input15.vcf.gz input16.vcf.gz input17.vcf.gz input18.vcf.gz input19.vcf.gz input20.vcf.gz input21.vcf.gz input22.vcf.gz input23.vcf.gz input24.vcf.gz; Date=Thu Apr 21 00:53:11 2022 +##bcftools_filterCommand=filter --regions-file regions_file.bed --output-type v --threads 1 input.vcf.gz; Date=Wed Sep 7 23:57:08 2022 +##bcftools_filterCommand=filter --include 'FILTER ~ "PASS" | FILTER ~ "MinMMQSdiff" | FILTER ~ "RefReadPos"' --output-type v --threads 1 input.vcf.gz; Date=Thu Sep 8 00:00:22 2022 +##bcftools_viewVersion=1.10.2+htslib-1.10.2 +##bcftools_viewCommand=view --output-type v; Date=Thu Sep 8 00:00:33 2022 +##bcftools_filterCommand=filter --include 'INFO/SS ~ "2"' --output-type v --threads 1 input.vcf.gz; Date=Thu Sep 8 00:00:44 2022 +##SnpSiftVersion="SnpSift 4.3t (build 2017-11-24 10:18), by Pablo Cingolani" +##SnpSiftCmd="SnpSift Annotate -info GENEINFO,PSEUDOGENEINFO,SAO,SSR,VC,NSF,NSM,NSN,SYN,U3,U5,ASS,DSS,INT,R3,R5,FREQ,COMMON,CLNVI,CLNORIGIN,CLNSIG,CLNDISDB,CLNDN,CLNREVSTAT,CLNACC dbSnp.vcf /home/galaxy/galaxy/database/datasets/001/336/dataset_1336409.dat" +##INFO=<ID=NSF,Number=0,Type=Flag,Description="Has non-synonymous frameshift A coding region variation where one allele in the set changes all downstream amino acids. FxnClass = 44"> +##INFO=<ID=R3,Number=0,Type=Flag,Description="In 3' gene region FxnCode = 13"> +##INFO=<ID=R5,Number=0,Type=Flag,Description="In 5' gene region FxnCode = 15"> +##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Variant Clinical Significance, 0 - Uncertain significance, 1 - not provided, 2 - Benign, 3 - Likely benign, 4 - Likely pathogenic, 5 - Pathogenic, 6 - drug response, 8 - confers sensitivity, 9 - risk-factor, 10 - association, 11 - protective, 12 - conflict, 13 - affects, 255 - other"> +##INFO=<ID=NSN,Number=0,Type=Flag,Description="Has non-synonymous nonsense A coding region variation where one allele in the set changes to STOP codon (TER). FxnClass = 41"> +##INFO=<ID=NSM,Number=0,Type=Flag,Description="Has non-synonymous missense A coding region variation where one allele in the set changes protein peptide. FxnClass = 42"> +##INFO=<ID=CLNORIGIN,Number=.,Type=String,Description="Allele Origin. One or more of the following values may be summed: 0 - unknown; 1 - germline; 2 - somatic; 4 - inherited; 8 - paternal; 16 - maternal; 32 - de-novo; 64 - biparental; 128 - uniparental; 256 - not-tested; 512 - tested-inconclusive; 1073741824 - other"> +##INFO=<ID=CLNREVSTAT,Number=.,Type=String,Description="ClinVar Review Status: no_assertion - No asserition provided by submitter, no_criteria - No assertion criteria provided by submitter, single - Classified by single submitter, mult - Classified by multiple submitters, conf - Criteria provided conflicting interpretations, exp - Reviewed by expert panel, guideline - Practice guideline"> +##INFO=<ID=COMMON,Number=0,Type=Flag,Description="RS is a common SNP. A common SNP is one that has at least one 1000Genomes population with a minor allele of frequency >= 1% and for which 2 or more founders contribute to that minor allele frequency."> +##INFO=<ID=FREQ,Number=.,Type=String,Description="An ordered list of allele frequencies as reported by various genomic studies starting with the reference allele followed by alternate alleles as ordered in the ALT column. When not already in the dbSNP allele set alleles from the studies are added to the ALT column. The minor allele which was previuosly reported in VCF as the GMAF is the second largest value in the list. This is the GMAF reported on the RefSNP and EntrezSNP pages and VariationReporter"> +##INFO=<ID=ASS,Number=0,Type=Flag,Description="In acceptor splice site FxnCode = 73"> +##INFO=<ID=U3,Number=0,Type=Flag,Description="In 3' UTR Location is in an untranslated region (UTR). FxnCode = 53"> +##INFO=<ID=U5,Number=0,Type=Flag,Description="In 5' UTR Location is in an untranslated region (UTR). FxnCode = 55"> +##INFO=<ID=CLNACC,Number=.,Type=String,Description="For each allele (comma delimited), this is a pipe-delimited list of the Clinvar RCV phenotype accession.version strings associated with that allele."> +##INFO=<ID=CLNDN,Number=.,Type=String,Description="Preferred ClinVar disease name"> +##INFO=<ID=DSS,Number=0,Type=Flag,Description="In donor splice-site FxnCode = 75"> +##INFO=<ID=SYN,Number=0,Type=Flag,Description="Has synonymous A coding region variation where one allele in the set does not change the encoded amino acid. FxnCode = 3"> +##INFO=<ID=CLNVI,Number=.,Type=String,Description="Variant Identifiers provided and maintained by organizations outside of NCBI, such as OMIM. Source and id separated by colon (:). Each identifier is separated by a vertical bar (|)"> +##INFO=<ID=VC,Number=1,Type=String,Description="Variation Class"> +##INFO=<ID=SAO,Number=1,Type=Integer,Description="Variant Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both"> +##INFO=<ID=PSEUDOGENEINFO,Number=1,Type=String,Description="Pairs each of pseudogene symbol:gene id. The pseudogene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|)"> +##INFO=<ID=CLNDISDB,Number=.,Type=String,Description="Variant disease database name and ID, separated by colon (:)"> +##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|). Does not include pseudogenes."> +##INFO=<ID=INT,Number=0,Type=Flag,Description="In Intron FxnCode = 6"> +##INFO=<ID=SSR,Number=1,Type=Integer,Description="Variant Suspect Reason Codes (may be more than one value added together) 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other"> +##bcftools_concatCommand=concat --allow-overlaps --min-PQ 30 --output-type v --threads 1 input0.vcf.gz input1.vcf.gz input2.vcf.gz input3.vcf.gz input4.vcf.gz input5.vcf.gz input6.vcf.gz input7.vcf.gz input8.vcf.gz input9.vcf.gz input10.vcf.gz input11.vcf.gz input12.vcf.gz input13.vcf.gz input14.vcf.gz input15.vcf.gz input16.vcf.gz input17.vcf.gz input18.vcf.gz input19.vcf.gz input20.vcf.gz input21.vcf.gz input22.vcf.gz input23.vcf.gz input24.vcf.gz; Date=Thu Sep 8 00:04:57 2022 +##bcftools_filterCommand=filter --include 'INFO/COMMON = 0' --output-type v --threads 1 input.vcf.gz; Date=Thu Sep 8 00:05:02 2022 +##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani" +##SnpEffCmd="SnpEff -i vcf -o vcf -stats /home/galaxy/galaxy/database/datasets/001/336/dataset_1336462.dat hg38 /home/galaxy/galaxy/database/datasets/001/336/dataset_1336460.dat " +##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'"> +##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +##INFO=<ID=ANNOVAR_DATE,Number=1,Type=String,Description="Flag the start of ANNOVAR annotation for one alternative allele"> +##INFO=<ID=cosmic70,Number=.,Type=String,Description="cosmic70 annotation provided by ANNOVAR"> +##INFO=<ID=SIFT_score,Number=.,Type=String,Description="SIFT_score annotation provided by ANNOVAR"> +##INFO=<ID=SIFT_pred,Number=.,Type=String,Description="SIFT_pred annotation provided by ANNOVAR"> +##INFO=<ID=Polyphen2_HDIV_score,Number=.,Type=String,Description="Polyphen2_HDIV_score annotation provided by ANNOVAR"> +##INFO=<ID=Polyphen2_HDIV_pred,Number=.,Type=String,Description="Polyphen2_HDIV_pred annotation provided by ANNOVAR"> +##INFO=<ID=Polyphen2_HVAR_score,Number=.,Type=String,Description="Polyphen2_HVAR_score annotation provided by ANNOVAR"> +##INFO=<ID=Polyphen2_HVAR_pred,Number=.,Type=String,Description="Polyphen2_HVAR_pred annotation provided by ANNOVAR"> +##INFO=<ID=LRT_score,Number=.,Type=String,Description="LRT_score annotation provided by ANNOVAR"> +##INFO=<ID=LRT_pred,Number=.,Type=String,Description="LRT_pred annotation provided by ANNOVAR"> +##INFO=<ID=MutationTaster_score,Number=.,Type=String,Description="MutationTaster_score annotation provided by ANNOVAR"> +##INFO=<ID=MutationTaster_pred,Number=.,Type=String,Description="MutationTaster_pred annotation provided by ANNOVAR"> +##INFO=<ID=MutationAssessor_score,Number=.,Type=String,Description="MutationAssessor_score annotation provided by ANNOVAR"> +##INFO=<ID=MutationAssessor_pred,Number=.,Type=String,Description="MutationAssessor_pred annotation provided by ANNOVAR"> +##INFO=<ID=FATHMM_score,Number=.,Type=String,Description="FATHMM_score annotation provided by ANNOVAR"> +##INFO=<ID=FATHMM_pred,Number=.,Type=String,Description="FATHMM_pred annotation provided by ANNOVAR"> +##INFO=<ID=RadialSVM_score,Number=.,Type=String,Description="RadialSVM_score annotation provided by ANNOVAR"> +##INFO=<ID=RadialSVM_pred,Number=.,Type=String,Description="RadialSVM_pred annotation provided by ANNOVAR"> +##INFO=<ID=LR_score,Number=.,Type=String,Description="LR_score annotation provided by ANNOVAR"> +##INFO=<ID=LR_pred,Number=.,Type=String,Description="LR_pred annotation provided by ANNOVAR"> +##INFO=<ID=VEST3_score,Number=.,Type=String,Description="VEST3_score annotation provided by ANNOVAR"> +##INFO=<ID=CADD_raw,Number=.,Type=String,Description="CADD_raw annotation provided by ANNOVAR"> +##INFO=<ID=CADD_phred,Number=.,Type=String,Description="CADD_phred annotation provided by ANNOVAR"> +##INFO=<ID=GERP++_RS,Number=.,Type=String,Description="GERP++_RS annotation provided by ANNOVAR"> +##INFO=<ID=phyloP46way_placental,Number=.,Type=String,Description="phyloP46way_placental annotation provided by ANNOVAR"> +##INFO=<ID=phyloP100way_vertebrate,Number=.,Type=String,Description="phyloP100way_vertebrate annotation provided by ANNOVAR"> +##INFO=<ID=SiPhy_29way_logOdds,Number=.,Type=String,Description="SiPhy_29way_logOdds annotation provided by ANNOVAR"> +##INFO=<ID=CLNALLELEID,Number=.,Type=String,Description="CLNALLELEID annotation provided by ANNOVAR"> +##INFO=<ID=ALLELE_END,Number=0,Type=Flag,Description="Flag the end of ANNOVAR annotation for one alternative allele"> +##bcftools_filterCommand=filter --include 'INFO/LOF != "." | INFO/CLNSIG != "." | INFO/cosmic70 != "." | INFO/Polyphen2_HDIV_pred != "." | INFO/LRT_pred != "." | INFO/MutationTaster_pred != "." | INFO/MutationAssessor_pred != "." | INFO/FATHMM_pred != "."' --output-type v --threads 1 input.vcf.gz; Date=Thu Sep 8 00:06:53 2022 +##SnpEffCmd="SnpEff -i vcf -o vcf -stats /home/galaxy/galaxy/database/datasets/001/336/dataset_1336466.dat hg38 /home/galaxy/galaxy/database/datasets/001/336/dataset_1336464.dat " +##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' "> +##FORMAT=<ID=VAF,Number=R,Type=float,Description="VariantAllele Frequency"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 01004_normal 01004_tumor +chr1 11650684 . A C . PASS DP=47;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11479 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:19:19,0:12,0:7,0:0.000 0/1:.:28:24,4:14,1:10,3:0.143 +chr1 16058496 rs1323290807 A G . PASS DP=142;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.099679;GENEINFO=FAM131C:348487;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:39:39,0:19,0:20,0:0.000 0/1:.:103:96,7:48,6:48,1:0.068 +chr1 27012594 rs1310186400 A C . PASS DP=54;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.090013;FREQ=GnomAD_exomes:1,.,7.598e-06|TOMMO:0.9985,0.001492,.;GENEINFO=TENT5B:115572;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:17:17,0:7,0:10,0:0.000 0/1:.:37:31,6:18,1:13,5:0.162 +chr1 44650749 rs201065980 G A . PASS DP=103;SOMATIC;SS=2;SSC=66;GPV=1;SPV=2.1118e-07;FREQ=1000Genomes:0.9998,0.0001997|ExAC:0.9999,0.0001247|GnomAD:1,2.139e-05|GnomAD_exomes:0.9999,0.0001238|Korea1K:0.9995,0.0005459|TOMMO:0.9994,0.0005967|TOPMED:1,2.645e-05|dbGaP_PopFreq:0.9999,8.681e-05;GENEINFO=RNF220:55182;NSM;R3;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:26:26,0:15,0:11,0:0.000 0/1:.:77:37,40:16,16:21,24:0.519 +chr1 48736294 . C CT . MinMMQSdiff DP=149;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10454;INDEL;LOF=(BEND5|BEND5|2|1.00) GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:46:45,0:25,0:20,0:0.000 0/1:.:103:95,6:44,4:51,2:0.059 +chr1 167553617 . T C . PASS DP=35;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.1143 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:14:14,0:10,0:4,0:0.000 0/1:.:21:17,4:6,1:11,3:0.190 +chr1 181798751 . A G . PASS DP=63;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10662 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:22:22,0:12,0:10,0:0.000 0/1:.:41:36,5:17,4:19,1:0.122 +chr1 200998483 rs777255666 A C . PASS DP=111;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11947;FREQ=ExAC:1,8.281e-06|Korea1K:0.9973,0.002729;GENEINFO=KIF21B:23046;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:28:28,0:18,0:10,0:0.000 0/1:.:83:75,7:44,1:31,6:0.085 +chr1 235138181 . CA C . MinMMQSdiff DP=128;SOMATIC;SS=2;SSC=15;GPV=1;SPV=0.028543;INDEL GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:50:42,3:21,3:21,0:0.067 0/1:.:78:60,16:31,8:29,8:0.211 +chr1 235775088 . TA T . MinMMQSdiff DP=181;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.086694;INDEL GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:53:51,0:25,0:26,0:0.000 0/1:.:128:118,7:63,3:55,4:0.056 +chr2 3702436 . T C . PASS DP=100;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.069291 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:35:35,0:27,0:8,0:0.000 0/1:.:65:59,6:41,1:18,5:0.092 +chr2 5693166 . A G . PASS DP=59;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.047667 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:13:13,0:5,0:8,0:0.000 0/1:.:46:35,11:15,9:20,2:0.239 +chr2 30232202 rs1677600959 A G . PASS DP=25;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11647;FREQ=GnomAD:1,8.673e-06|dbGaP_PopFreq:1,0;GENEINFO=LBH:81606;INT;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:8:8,0:6,0:2,0:0.000 0/1:.:17:12,5:10,4:2,1:0.294 +chr2 152148302 . TA T . PASS DP=118;SOMATIC;SS=2;SSC=12;GPV=1;SPV=0.057995;INDEL GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:30:29,0:12,0:17,0:0.000 0/1:.:88:73,9:45,5:28,4:0.110 +chr2 229271024 rs1690724066 T C . PASS DP=58;SOMATIC;SS=2;SSC=15;GPV=1;SPV=0.027364;FREQ=TOMMO:0.9987,0.001313;GENEINFO=PID1:55022;NSM;R5;SSR=0;U5;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:25:25,0:11,0:14,0:0.000 0/1:.:33:27,6:9,2:18,4:0.182 +chr3 24118973 . G GT . MinMMQSdiff DP=53;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.044075;INDEL GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:23:17,1:12,0:5,1:0.056 0/1:.:30:15,7:12,4:3,3:0.318 +chr3 32953733 rs1575380659 T G . PASS DP=166;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.096467;FREQ=Korea1K:0.988,0.01201|dbGaP_PopFreq:1,4.677e-05;GENEINFO=CCR4:1233;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:46:46,0:22,0:24,0:0.000 0/1:.:120:112,7:46,4:66,3:0.059 +chr3 38485666 . CTTT C . PASS DP=33;SOMATIC;SS=2;SSC=16;GPV=1;SPV=0.023839;INDEL GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:12:6,0:4,0:2,0:0.000 0/1:.:21:6,8:4,3:2,5:0.571 +chr3 108505838 . CA C . MinMMQSdiff DP=164;SOMATIC;SS=2;SSC=14;GPV=1;SPV=0.037929;INDEL GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:44:36,0:20,0:16,0:0.000 0/1:.:120:98,11:61,6:37,5:0.101 +chr3 129315500 rs2071293837 T G . PASS DP=29;SOMATIC;SS=2;SSC=23;GPV=1;SPV=0.0041229;FREQ=TOMMO:0.9963,0.003703;GENEINFO=H1-10:8971|H1-10-AS1:339942;NSM;R5;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:14:14,0:8,0:6,0:0.000 0/1:.:15:8,7:5,4:3,3:0.467 +chr4 122187879 . A AT . MinMMQSdiff DP=164;SOMATIC;SS=2;SSC=17;GPV=1;SPV=0.019764;INDEL;LOF=(KIAA1109|KIAA1109|1|1.00) GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:39:37,0:22,0:15,0:0.000 0/1:.:125:107,14:56,5:51,9:0.116 +chr5 137677661 . CA C . MinMMQSdiff DP=115;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10535;INDEL GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:29:21,0:12,0:9,0:0.000 0/1:.:86:69,9:37,6:32,3:0.115 +chr5 160092476 rs1755181710 T C . PASS DP=139;SOMATIC;SS=2;SSC=18;GPV=1;SPV=0.013;FREQ=TOMMO:0.9967,0.003282;GENEINFO=PWWP2A:114825;INT;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:47:47,0:25,0:22,0:0.000 0/1:.:92:81,10:22,9:59,1:0.110 +chr5 177257228 . C CT . MinMMQSdiff DP=58;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.1043;INDEL GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:18:13,0:5,0:8,0:0.000 0/1:.:40:25,6:15,3:10,3:0.194 +chr6 35823448 . T TAC . PASS DP=62;SOMATIC;SS=2;SSC=15;GPV=1;SPV=0.026386;INDEL GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:18:16,1:12,0:4,1:0.059 0/1:.:44:26,13:16,11:10,2:0.333 +chr6 36200360 . A G . PASS DP=113;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.065653 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:31:31,0:16,0:15,0:0.000 0/1:.:82:72,8:37,4:35,4:0.100 +chr6 39934360 . T C . PASS DP=48;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11077 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:16:16,0:9,0:7,0:0.000 0/1:.:32:26,5:14,1:12,4:0.161 +chr6 87701546 . T G . PASS DP=34;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.044477 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:17:17,0:7,0:10,0:0.000 0/1:.:17:12,4:3,2:9,2:0.250 +chr6 113859846 . A G . PASS DP=21;SOMATIC;SS=2;SSC=12;GPV=1;SPV=0.055138 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:10:10,0:2,0:8,0:0.000 0/1:.:11:7,4:7,4:0,0:0.364 +chr6 138107153 . T C . PASS DP=52;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.077483 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:20:20,0:8,0:12,0:0.000 0/1:.:32:27,5:4,1:23,4:0.156 +chr6 152278138 rs2093774796 C T . PASS DP=103;SOMATIC;SS=2;SSC=57;GPV=1;SPV=1.9582e-06;FREQ=GnomAD:1,7.127e-06|TOPMED:1,3.778e-06|dbGaP_PopFreq:1,0;GENEINFO=SYNE1:23345;NSM;R5;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:21:21,0:15,0:6,0:0.000 0/1:.:82:39,43:18,25:21,18:0.524 +chr7 44082410 rs2096202919 A C . PASS DP=62;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.043;FREQ=GnomAD:1,7.144e-06|TOPMED:1,1.511e-05|dbGaP_PopFreq:1,0;GENEINFO=POLM:27434;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:28:28,0:10,0:18,0:0.000 0/1:.:34:29,5:13,1:16,4:0.147 +chr7 100577295 . A C . PASS DP=66;SOMATIC;SS=2;SSC=17;GPV=1;SPV=0.01619 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:22:22,0:12,0:10,0:0.000 0/1:.:44:33,9:23,2:10,7:0.214 +chr7 129225249 . A G . PASS DP=19;SOMATIC;SS=2;SSC=12;GPV=1;SPV=0.05418 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:9:9,0:3,0:6,0:0.000 0/1:.:10:6,4:6,4:0,0:0.400 +chr7 137015017 . A C . PASS DP=154;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.092245 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:49:49,0:25,0:24,0:0.000 0/1:.:105:97,6:56,1:41,5:0.058 +chr8 64616285 . G GA . PASS DP=152;SOMATIC;SS=2;SSC=16;GPV=1;SPV=0.022125;INDEL GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:53:49,0:23,0:26,0:0.000 0/1:.:99:88,9:52,7:36,2:0.093 +chr8 85662359 rs1814217731 A G . PASS DP=188;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11249;FREQ=dbGaP_PopFreq:1,0;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:56:56,0:13,0:43,0:0.000 0/1:.:132:124,6:20,5:104,1:0.046 +chr8 144437095 . T G . PASS DP=103;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10209 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:37:37,0:19,0:18,0:0.000 0/1:.:66:61,5:24,3:37,2:0.076 +chr9 34371544 . A C . PASS DP=83;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.091683 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:30:30,0:12,0:18,0:0.000 0/1:.:53:46,5:27,1:19,4:0.098 +chr9 93257022 rs1843418763 T C . PASS DP=88;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11696;FREQ=dbGaP_PopFreq:1,3.13e-05;GENEINFO=WNK2:65268;SSR=0;SYN;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:30:30,0:18,0:12,0:0.000 0/1:.:58:53,5:39,1:14,4:0.086 +chr9 93257030 rs745449856 A C . PASS DP=91;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10193;FREQ=ExAC:1,1.163e-05,.|Korea1K:0.9984,0.001638,.|TOPMED:1,7.964e-06,.|dbGaP_PopFreq:0.9999,7.117e-05,0;GENEINFO=WNK2:65268;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:28:28,0:17,0:11,0:0.000 0/1:.:63:57,6:35,2:22,4:0.095 +chr9 122893029 . TA T . MinMMQSdiff DP=159;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.046021;INDEL GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:42:37,1:18,1:19,0:0.026 0/1:.:117:87,14:52,8:35,6:0.139 +chr9 128633818 . T C . PASS DP=133;SOMATIC;SS=2;SSC=12;GPV=1;SPV=0.055306 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:39:39,0:20,0:19,0:0.000 0/1:.:94:85,8:51,1:34,7:0.086 +chr9 136763918 . A G . PASS DP=109;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.080707 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:32:32,0:18,0:14,0:0.000 0/1:.:77:70,7:30,6:40,1:0.091 +chr9 137743352 . CT C . MinMMQSdiff DP=164;SOMATIC;SS=2;SSC=17;GPV=1;SPV=0.018344;INDEL GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:43:39,1:23,1:16,0:0.025 0/1:.:121:95,18:54,11:41,7:0.159 +chr10 11463685 . A G . PASS DP=102;SOMATIC;SS=2;SSC=16;GPV=1;SPV=0.0231 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:41:40,1:23,1:17,0:0.024 0/1:.:61:51,10:18,9:33,1:0.164 +chr10 26697814 . A G . PASS DP=46;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11779 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:18:18,0:6,0:12,0:0.000 0/1:.:28:23,4:8,3:15,1:0.148 +chr10 75108094 . T C . PASS DP=93;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.063155 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:29:29,0:15,0:14,0:0.000 0/1:.:64:56,7:34,1:22,6:0.111 +chr10 119030064 rs1209333669 A C . PASS DP=29;SOMATIC;SS=2;SSC=19;GPV=1;SPV=0.010536;FREQ=TOPMED:1,.,2.389e-05|dbGaP_PopFreq:1,.,0;GENEINFO=NANOS1:340719;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:14:14,0:12,0:2,0:0.000 0/1:.:15:9,6:5,3:4,3:0.400 +chr11 6603418 . A G . PASS DP=78;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10724 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:27:27,0:13,0:14,0:0.000 0/1:.:51:45,5:16,4:29,1:0.100 +chr11 32392004 . T TTGGGAGG . MinMMQSdiff DP=150;SOMATIC;SS=2;SSC=101;GPV=1;SPV=6.8811e-11;INDEL;LOF=(WT1|WT1|5|1.00) GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:41:41,0:31,0:10,0:0.000 0/1:.:109:52,55:27,27:25,28:0.514 +chr11 66333308 . A G . PASS DP=95;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.087528 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:24:24,0:10,0:14,0:0.000 0/1:.:71:63,8:29,6:34,2:0.113 +chr11 66591673 rs1590825346 A C . PASS DP=114;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11476;FREQ=Korea1K:0.9967,0.003275;GENEINFO=CCS:9973|CCDC87:55231;NSM;R5;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:39:39,0:19,0:20,0:0.000 0/1:.:75:69,5:47,1:22,4:0.068 +chr12 39293733 . GA G . PASS DP=108;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.046488;INDEL GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:28:28,0:19,0:9,0:0.000 0/1:.:80:64,9:36,6:28,3:0.123 +chr12 52520086 . A G . PASS DP=83;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11591 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:28:28,0:14,0:14,0:0.000 0/1:.:55:49,5:35,4:14,1:0.093 +chr12 113181030 . A C . PASS DP=116;SOMATIC;SS=2;SSC=95;GPV=1;SPV=2.8536e-10 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:39:39,0:16,0:23,0:0.000 0/1:.:77:36,41:16,22:20,19:0.532 +chr12 122183296 . T G . PASS DP=60;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.046436;LOF=(LRRC43|LRRC43|2|0.50) GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:23:23,0:9,0:14,0:0.000 0/1:.:37:31,6:12,5:19,1:0.162 +chr14 91969289 . TA T . MinMMQSdiff DP=156;SOMATIC;SS=2;SSC=15;GPV=1;SPV=0.02796;INDEL GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:61:58,0:31,0:27,0:0.000 0/1:.:95:83,7:38,5:45,2:0.078 +chr15 41511296 . A G . PASS DP=43;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.1021 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:15:15,0:5,0:10,0:0.000 0/1:.:28:23,5:10,3:13,2:0.179 +chr15 50609732 . TA T . MinMMQSdiff DP=191;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.078004;INDEL GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:51:49,0:23,0:26,0:0.000 0/1:.:140:126,8:64,5:62,3:0.060 +chr15 70891968 . T C . PASS DP=100;SOMATIC;SS=2;SSC=12;GPV=1;SPV=0.05157 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:38:38,0:23,0:15,0:0.000 0/1:.:62:56,6:31,2:25,4:0.097 +chr16 662321 . T C . PASS DP=92;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11106 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:32:32,0:20,0:12,0:0.000 0/1:.:60:55,5:29,2:26,3:0.083 +chr16 10907873 rs2039285618 A G . PASS DP=77;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.096829;FREQ=TOMMO:0.9996,0.000358;GENEINFO=CIITA:4261;INT;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:24:24,0:10,0:14,0:0.000 0/1:.:53:47,6:28,1:19,5:0.113 +chr16 30582843 rs1597148926 T G . PASS DP=71;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11095;FREQ=Korea1K:0.9973,0.002738;GENEINFO=ZNF785:146540;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:21:21,0:10,0:11,0:0.000 0/1:.:50:44,6:5,5:39,1:0.120 +chr16 30659613 rs2052429106 A G . PASS DP=20;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.068111;FREQ=dbGaP_PopFreq:1,0;GENEINFO=FBRS:64319;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:9:9,0:5,0:4,0:0.000 0/1:.:11:7,4:4,3:3,1:0.364 +chr16 57077971 rs762970987 A C . PASS DP=98;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.07847;FREQ=ExAC:1,.,8.548e-06|GnomAD_exomes:1,.,4.01e-06|dbGaP_PopFreq:1,0,.;GENEINFO=NLRC5:84166;NSM;R3;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:33:33,0:15,0:18,0:0.000 0/1:.:65:59,6:30,1:29,5:0.092 +chr16 67543151 . A G . PASS DP=99;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11701 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:29:29,0:14,0:15,0:0.000 0/1:.:70:64,6:27,5:37,1:0.086 +chr16 84196276 . A C . PASS DP=68;SOMATIC;SS=2;SSC=14;GPV=1;SPV=0.03324 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:25:25,0:16,0:9,0:0.000 0/1:.:43:36,7:10,5:26,2:0.163 +chr16 85657427 rs2052056269 T C . PASS DP=67;SOMATIC;SS=2;SSC=14;GPV=1;SPV=0.033048;FREQ=TOMMO:0.999,0.0009547;GENEINFO=GSE1:23199;NSM;R3;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:22:22,0:17,0:5,0:0.000 0/1:.:45:37,8:24,1:13,7:0.178 +chr17 7235658 rs1597560221 A C . PASS DP=148;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.072541;FREQ=Korea1K:0.9973,0.002729;GENEINFO=DVL2:1856|PHF23:79142;NSM;R5;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:45:45,0:21,0:24,0:0.000 0/1:.:103:95,7:62,1:33,6:0.069 +chr17 56834826 . T C . PASS DP=52;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11622 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:21:21,0:16,0:5,0:0.000 0/1:.:31:27,4:15,2:12,2:0.129 +chr17 74525837 . A G . PASS DP=136;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10968 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:36:36,0:20,0:16,0:0.000 0/1:.:100:93,7:40,6:53,1:0.070 +chr17 81665449 . A G . PASS DP=79;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.084997 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:20:20,0:10,0:10,0:0.000 0/1:.:59:51,8:14,7:37,1:0.136 +chr18 23136360 . T G . PASS DP=31;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.048889 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:15:14,0:4,0:10,0:0.000 0/1:.:16:10,4:6,3:4,1:0.286 +chr18 33943180 . TA T . MinMMQSdiff DP=120;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.079905;INDEL GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:39:39,0:29,0:10,0:0.000 0/1:.:81:71,6:37,5:34,1:0.078 +chr18 57436318 . A G . PASS DP=55;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.091832 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:13:13,0:7,0:6,0:0.000 0/1:.:42:33,8:9,7:24,1:0.195 +chr19 3753833 . T C . PASS DP=49;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.042387 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:12:12,0:6,0:6,0:0.000 0/1:.:37:27,10:18,1:9,9:0.270 +chr19 6375414 . T C . PASS DP=42;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11302 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:17:17,0:9,0:8,0:0.000 0/1:.:25:21,4:10,1:11,3:0.160 +chr19 6375439 . A C . PASS DP=41;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11076 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:15:15,0:8,0:7,0:0.000 0/1:.:26:18,4:8,1:10,3:0.182 +chr19 10092121 . A C . PASS DP=121;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10576 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:37:37,0:16,0:21,0:0.000 0/1:.:84:78,6:51,1:27,5:0.071 +chr19 16878242 . A G . PASS DP=84;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.099575 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:26:26,0:11,0:15,0:0.000 0/1:.:58:52,6:17,5:35,1:0.103 +chr19 17300950 rs1223479129 C G . PASS DP=87;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.049205;FREQ=GnomAD_exomes:1,4.023e-06,.|TOMMO:0.9992,.,0.0008354;GENEINFO=MRPL34:64981|ABHD8:79575;NSM;R5;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:29:29,0:14,0:15,0:0.000 0/1:.:58:50,7:15,6:35,1:0.123 +chr19 17830104 . T C . PASS DP=96;SOMATIC;SS=2;SSC=14;GPV=1;SPV=0.03365 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:26:26,0:13,0:13,0:0.000 0/1:.:70:59,10:33,1:26,9:0.145 +chr19 39425108 . A C . PASS DP=91;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.047715 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:31:31,0:13,0:18,0:0.000 0/1:.:60:53,7:27,3:26,4:0.117 +chr19 42225307 rs757193095 A C . PASS DP=61;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11061;FREQ=ExAC:0.9999,0.0001304;GENEINFO=ZNF526:116115;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:21:21,0:12,0:9,0:0.000 0/1:.:40:35,5:10,4:25,1:0.125 +chr19 45785825 . A C . PASS DP=65;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.063509 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:23:23,0:11,0:12,0:0.000 0/1:.:42:36,6:21,2:15,4:0.143 +chr19 46787914 rs2055198734 T G . PASS DP=61;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11061;FREQ=TOMMO:0.9998,0.000179;GENEINFO=SLC1A5:6510;NSM;R5;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:21:21,0:13,0:8,0:0.000 0/1:.:40:35,5:21,4:14,1:0.125 +chr19 47754611 . A C . PASS DP=44;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10935 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:15:15,0:8,0:7,0:0.000 0/1:.:29:24,5:8,4:16,1:0.172 +chr19 48837393 . T G . PASS DP=111;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.091093 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:31:31,0:14,0:17,0:0.000 0/1:.:80:72,7:23,6:49,1:0.089 +chr19 49651647 rs7251334 A C . PASS DP=37;SOMATIC;SS=2;SSC=15;GPV=1;SPV=0.029941;FREQ=1000Genomes:0.003195,0.9968|ALSPAC:0.006746,0.9933|Estonian:0.009865,0.9901|ExAC:0.01316,0.9868|GENOME_DK:0.075,0.925|GnomAD:0.009591,0.9904|GnomAD_exomes:0.01297,0.987|KOREAN:0.0003544,0.9996|Korea1K:0,1|NorthernSweden:0.01333,0.9867|Qatari:0.009259,0.9907|SGDP_PRJ:0.00369,0.9963|Siberian:0,1|TOMMO:5.996e-05,0.9999|TOPMED:0.009007,0.991|TWINSUK:0.002697,0.9973|dbGaP_PopFreq:0.01097,0.989;GENEINFO=SCAF1:58506;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:10:9,1:4,1:5,0:0.100 0/1:.:27:13,13:7,7:6,6:0.500 +chr20 36436128 . A G . PASS DP=80;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.085947 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:26:26,0:8,0:18,0:0.000 0/1:.:54:48,6:13,5:35,1:0.111 +chr20 36436160 . A G . PASS DP=85;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11645 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:29:29,0:12,0:17,0:0.000 0/1:.:56:51,5:21,4:30,1:0.089 +chr20 38926705 . A G . PASS DP=32;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10779 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:13:13,0:6,0:7,0:0.000 0/1:.:19:15,4:2,3:13,1:0.211 +chr20 49850763 . G GT . MinMMQSdiff DP=138;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10754;INDEL;LOF=(SLC9A8|SLC9A8|6|0.17) GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:37:36,0:20,0:16,0:0.000 0/1:.:101:92,7:41,2:51,5:0.071 +chr20 58470723 rs780513473 T C . PASS DP=68;SOMATIC;SS=2;SSC=15;GPV=1;SPV=0.027829;FREQ=ExAC:0.9997,0.0002659|Korea1K:0.9961,0.003855;GENEINFO=APCDD1L:164284;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:26:26,0:12,0:14,0:0.000 0/1:.:42:35,7:11,1:24,6:0.167 +chr20 63962289 . A G . PASS DP=119;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.074509 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:32:32,0:12,0:20,0:0.000 0/1:.:87:79,8:28,7:51,1:0.092 +chr21 44294402 . A G . PASS DP=39;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.093821 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:10:10,0:9,0:1,0:0.000 0/1:.:29:21,7:20,7:1,0:0.250 +chr21 46391311 . A G . PASS DP=98;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.07847 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:33:33,0:13,0:20,0:0.000 0/1:.:65:59,6:19,4:40,2:0.092 +chr22 21642940 rs779759705 A G . PASS DP=54;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.086849;FREQ=ExAC:0.9999,7.462e-05|GnomAD:1,7.143e-06|GnomAD_exomes:1,2.219e-05|TOPMED:1,7.556e-06|dbGaP_PopFreq:1,0;GENEINFO=SDF2L1:23753;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:15:15,0:9,0:6,0:0.000 0/1:.:39:32,7:16,6:16,1:0.179 +chr22 24095973 . A G . PASS DP=135;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11972 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:46:46,0:16,0:30,0:0.000 0/1:.:89:84,5:29,4:55,1:0.056 +chr22 29050610 . T C . PASS DP=75;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.089227 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:21:21,0:14,0:7,0:0.000 0/1:.:54:47,7:36,1:11,6:0.130 +chr22 37373680 . T C . PASS DP=91;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10913 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:27:27,0:15,0:12,0:0.000 0/1:.:64:57,6:34,4:23,2:0.095 +chrX 13713103 . CA C . MinMMQSdiff DP=118;SOMATIC;SS=2;SSC=12;GPV=1;SPV=0.05176;INDEL GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:39:32,0:16,0:16,0:0.000 0/1:.:79:67,8:28,6:39,2:0.107 +chrX 22111531 . T C . PASS DP=154;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.048459 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:53:53,0:31,0:22,0:0.000 0/1:.:101:94,7:42,6:52,1:0.069 +chrX 71132767 . C CCTCTT . MinMMQSdiff DP=105;SOMATIC;SS=2;SSC=14;GPV=1;SPV=0.035112;INDEL GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:31:27,1:8,0:19,1:0.036 0/1:.:74:52,13:24,8:28,5:0.200 +chrX 75431524 . T TA . PASS DP=201;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.066007;INDEL GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:58:54,0:25,0:29,0:0.000 0/1:.:143:129,8:61,3:68,5:0.058 +chrX 153647994 . A G . PASS DP=31;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.097251 GT:GQ:DP:AD:ADF:ADR:VAF 0/0:.:13:13,0:5,0:8,0:0.000 0/1:.:18:14,4:4,3:10,1:0.222
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcf_1.vcf Mon Nov 28 21:59:34 2022 +0000 @@ -0,0 +1,188 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=PASS,Description="All filters passed"> +##reference=/home/galaxy/galaxy/tool-data/hg38-bgi-light/sam_indexes/hg38-bgi-light/hg38-bgi-light.fa +##source=varscan.py +##contig=<ID=chr1,length=248956422> +##contig=<ID=chr10,length=133797422> +##contig=<ID=chr11,length=135086622> +##contig=<ID=chr12,length=133275309> +##contig=<ID=chr13,length=114364328> +##contig=<ID=chr14,length=107043718> +##contig=<ID=chr15,length=101991189> +##contig=<ID=chr16,length=90338345> +##contig=<ID=chr17,length=83257441> +##contig=<ID=chr18,length=80373285> +##contig=<ID=chr19,length=58617616> +##contig=<ID=chr2,length=242193529> +##contig=<ID=chr20,length=64444167> +##contig=<ID=chr21,length=46709983> +##contig=<ID=chr22,length=50818468> +##contig=<ID=chr3,length=198295559> +##contig=<ID=chr4,length=190214555> +##contig=<ID=chr5,length=181538259> +##contig=<ID=chr6,length=170805979> +##contig=<ID=chr7,length=159345973> +##contig=<ID=chr8,length=145138636> +##contig=<ID=chr9,length=138394717> +##contig=<ID=chrM,length=16569> +##contig=<ID=chrX,length=156040895> +##contig=<ID=chrY,length=57227415> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases"> +##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation"> +##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)"> +##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value"> +##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls"> +##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls"> +##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand"> +##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position"> +##FILTER=<ID=VarCount,Description="Fewer than 4 variant-supporting reads"> +##FILTER=<ID=VarFreq,Description="Variant allele frequency below 0.05"> +##FILTER=<ID=VarAvgRL,Description="Average clipped length of variant-supporting reads < 90"> +##FILTER=<ID=VarReadPos,Description="Relative average read position < 0.1"> +##FILTER=<ID=VarDist3,Description="Average distance to effective 3' end < 0.1"> +##FILTER=<ID=VarMMQS,Description="Average mismatch quality sum for variant reads > 100"> +##FILTER=<ID=VarMapQual,Description="Average mapping quality of variant reads < 15"> +##FILTER=<ID=VarBaseQual,Description="Average base quality of variant reads < 15"> +##FILTER=<ID=Strand,Description="Strand representation of variant reads < 0.01"> +##FILTER=<ID=RefAvgRL,Description="Average clipped length of ref-supporting reads < 90"> +##FILTER=<ID=RefReadPos,Description="Relative average read position < 0.1"> +##FILTER=<ID=RefDist3,Description="Average distance to effective 3' end < 0.1"> +##FILTER=<ID=RefMapQual,Description="Average mapping quality of reference reads < 15"> +##FILTER=<ID=RefBaseQual,Description="Average base quality of ref-supporting reads < 15"> +##FILTER=<ID=RefMMQS,Description="Average mismatch quality sum for ref-supporting reads > 100"> +##FILTER=<ID=MMQSdiff,Description="Mismatch quality sum difference (var - ref) > 50"> +##FILTER=<ID=MinMMQSdiff,Description="Mismatch quality sum difference (var - ref) < 50"> +##FILTER=<ID=MapQualDiff,Description="Mapping quality difference (ref - var) > 50"> +##FILTER=<ID=MaxBAQdiff,Description="Average base quality difference (ref - var) > 50"> +##FILTER=<ID=ReadLenDiff,Description="Average supporting read length difference (ref - var) > 0.25"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype code"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth"> +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele"> +##FORMAT=<ID=ADF,Number=R,Type=Integer,Description="Read depth for each allele on the forward strand"> +##FORMAT=<ID=ADR,Number=R,Type=Integer,Description="Read depth for each allele on the reverse strand"> +##bcftools_filterVersion=1.10.2+htslib-1.10.2 +##bcftools_filterCommand=filter --include 'INFO/SPV < 0.12 | INFO/GPV < 0.12' --output-type v --threads 1 input.vcf.gz; Date=Thu Apr 21 00:18:01 2022 +##bcftools_filterCommand=filter --include 'FILTER ~ "PASS" | FILTER ~ "MinMMQSdiff" | FILTER ~ "RefReadPos"' --output-type v --threads 1 input.vcf.gz; Date=Wed Sep 7 20:48:58 2022 +##bcftools_viewVersion=1.10.2+htslib-1.10.2 +##bcftools_viewCommand=view --output-type v; Date=Wed Sep 7 20:49:09 2022 +##bcftools_filterCommand=filter --include 'INFO/SS ~ "2"' --output-type v --threads 1 input.vcf.gz; Date=Wed Sep 7 20:49:20 2022 +##SnpSiftVersion="SnpSift 4.3t (build 2017-11-24 10:18), by Pablo Cingolani" +##SnpSiftCmd="SnpSift Annotate -info GENEINFO,PSEUDOGENEINFO,SAO,SSR,VC,NSF,NSM,NSN,SYN,U3,U5,ASS,DSS,INT,R3,R5,FREQ,COMMON,CLNVI,CLNORIGIN,CLNSIG,CLNDISDB,CLNDN,CLNREVSTAT,CLNACC dbSnp.vcf /home/galaxy/galaxy/database/datasets/001/336/dataset_1336143.dat" +##INFO=<ID=NSF,Number=0,Type=Flag,Description="Has non-synonymous frameshift A coding region variation where one allele in the set changes all downstream amino acids. FxnClass = 44"> +##INFO=<ID=R3,Number=0,Type=Flag,Description="In 3' gene region FxnCode = 13"> +##INFO=<ID=R5,Number=0,Type=Flag,Description="In 5' gene region FxnCode = 15"> +##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Variant Clinical Significance, 0 - Uncertain significance, 1 - not provided, 2 - Benign, 3 - Likely benign, 4 - Likely pathogenic, 5 - Pathogenic, 6 - drug response, 8 - confers sensitivity, 9 - risk-factor, 10 - association, 11 - protective, 12 - conflict, 13 - affects, 255 - other"> +##INFO=<ID=NSN,Number=0,Type=Flag,Description="Has non-synonymous nonsense A coding region variation where one allele in the set changes to STOP codon (TER). FxnClass = 41"> +##INFO=<ID=NSM,Number=0,Type=Flag,Description="Has non-synonymous missense A coding region variation where one allele in the set changes protein peptide. FxnClass = 42"> +##INFO=<ID=CLNORIGIN,Number=.,Type=String,Description="Allele Origin. One or more of the following values may be summed: 0 - unknown; 1 - germline; 2 - somatic; 4 - inherited; 8 - paternal; 16 - maternal; 32 - de-novo; 64 - biparental; 128 - uniparental; 256 - not-tested; 512 - tested-inconclusive; 1073741824 - other"> +##INFO=<ID=CLNREVSTAT,Number=.,Type=String,Description="ClinVar Review Status: no_assertion - No asserition provided by submitter, no_criteria - No assertion criteria provided by submitter, single - Classified by single submitter, mult - Classified by multiple submitters, conf - Criteria provided conflicting interpretations, exp - Reviewed by expert panel, guideline - Practice guideline"> +##INFO=<ID=COMMON,Number=0,Type=Flag,Description="RS is a common SNP. A common SNP is one that has at least one 1000Genomes population with a minor allele of frequency >= 1% and for which 2 or more founders contribute to that minor allele frequency."> +##INFO=<ID=FREQ,Number=.,Type=String,Description="An ordered list of allele frequencies as reported by various genomic studies starting with the reference allele followed by alternate alleles as ordered in the ALT column. When not already in the dbSNP allele set alleles from the studies are added to the ALT column. The minor allele which was previuosly reported in VCF as the GMAF is the second largest value in the list. This is the GMAF reported on the RefSNP and EntrezSNP pages and VariationReporter"> +##INFO=<ID=ASS,Number=0,Type=Flag,Description="In acceptor splice site FxnCode = 73"> +##INFO=<ID=U3,Number=0,Type=Flag,Description="In 3' UTR Location is in an untranslated region (UTR). FxnCode = 53"> +##INFO=<ID=U5,Number=0,Type=Flag,Description="In 5' UTR Location is in an untranslated region (UTR). FxnCode = 55"> +##INFO=<ID=CLNACC,Number=.,Type=String,Description="For each allele (comma delimited), this is a pipe-delimited list of the Clinvar RCV phenotype accession.version strings associated with that allele."> +##INFO=<ID=CLNDN,Number=.,Type=String,Description="Preferred ClinVar disease name"> +##INFO=<ID=DSS,Number=0,Type=Flag,Description="In donor splice-site FxnCode = 75"> +##INFO=<ID=SYN,Number=0,Type=Flag,Description="Has synonymous A coding region variation where one allele in the set does not change the encoded amino acid. FxnCode = 3"> +##INFO=<ID=CLNVI,Number=.,Type=String,Description="Variant Identifiers provided and maintained by organizations outside of NCBI, such as OMIM. Source and id separated by colon (:). Each identifier is separated by a vertical bar (|)"> +##INFO=<ID=VC,Number=1,Type=String,Description="Variation Class"> +##INFO=<ID=SAO,Number=1,Type=Integer,Description="Variant Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both"> +##INFO=<ID=PSEUDOGENEINFO,Number=1,Type=String,Description="Pairs each of pseudogene symbol:gene id. The pseudogene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|)"> +##INFO=<ID=CLNDISDB,Number=.,Type=String,Description="Variant disease database name and ID, separated by colon (:)"> +##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|). Does not include pseudogenes."> +##INFO=<ID=INT,Number=0,Type=Flag,Description="In Intron FxnCode = 6"> +##INFO=<ID=SSR,Number=1,Type=Integer,Description="Variant Suspect Reason Codes (may be more than one value added together) 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other"> +##bcftools_concatVersion=1.10.2+htslib-1.10.2 +##bcftools_concatCommand=concat --allow-overlaps --min-PQ 30 --output-type v --threads 1 input0.vcf.gz input1.vcf.gz input2.vcf.gz input3.vcf.gz input4.vcf.gz input5.vcf.gz input6.vcf.gz input7.vcf.gz input8.vcf.gz input9.vcf.gz input10.vcf.gz input11.vcf.gz input12.vcf.gz input13.vcf.gz input14.vcf.gz input15.vcf.gz input16.vcf.gz input17.vcf.gz input18.vcf.gz input19.vcf.gz input20.vcf.gz input21.vcf.gz input22.vcf.gz input23.vcf.gz input24.vcf.gz; Date=Wed Sep 7 20:53:30 2022 +##bcftools_filterCommand=filter --include 'INFO/COMMON = 0' --output-type v --threads 1 input.vcf.gz; Date=Wed Sep 7 20:53:35 2022 +##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani" +##SnpEffCmd="SnpEff -i vcf -o vcf -stats /home/galaxy/galaxy/database/datasets/001/336/dataset_1336196.dat hg38 /home/galaxy/galaxy/database/datasets/001/336/dataset_1336194.dat " +##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'"> +##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +##INFO=<ID=ANNOVAR_DATE,Number=1,Type=String,Description="Flag the start of ANNOVAR annotation for one alternative allele"> +##INFO=<ID=cosmic70,Number=.,Type=String,Description="cosmic70 annotation provided by ANNOVAR"> +##INFO=<ID=SIFT_score,Number=.,Type=String,Description="SIFT_score annotation provided by ANNOVAR"> +##INFO=<ID=SIFT_pred,Number=.,Type=String,Description="SIFT_pred annotation provided by ANNOVAR"> +##INFO=<ID=Polyphen2_HDIV_score,Number=.,Type=String,Description="Polyphen2_HDIV_score annotation provided by ANNOVAR"> +##INFO=<ID=Polyphen2_HDIV_pred,Number=.,Type=String,Description="Polyphen2_HDIV_pred annotation provided by ANNOVAR"> +##INFO=<ID=Polyphen2_HVAR_score,Number=.,Type=String,Description="Polyphen2_HVAR_score annotation provided by ANNOVAR"> +##INFO=<ID=Polyphen2_HVAR_pred,Number=.,Type=String,Description="Polyphen2_HVAR_pred annotation provided by ANNOVAR"> +##INFO=<ID=LRT_score,Number=.,Type=String,Description="LRT_score annotation provided by ANNOVAR"> +##INFO=<ID=LRT_pred,Number=.,Type=String,Description="LRT_pred annotation provided by ANNOVAR"> +##INFO=<ID=MutationTaster_score,Number=.,Type=String,Description="MutationTaster_score annotation provided by ANNOVAR"> +##INFO=<ID=MutationTaster_pred,Number=.,Type=String,Description="MutationTaster_pred annotation provided by ANNOVAR"> +##INFO=<ID=MutationAssessor_score,Number=.,Type=String,Description="MutationAssessor_score annotation provided by ANNOVAR"> +##INFO=<ID=MutationAssessor_pred,Number=.,Type=String,Description="MutationAssessor_pred annotation provided by ANNOVAR"> +##INFO=<ID=FATHMM_score,Number=.,Type=String,Description="FATHMM_score annotation provided by ANNOVAR"> +##INFO=<ID=FATHMM_pred,Number=.,Type=String,Description="FATHMM_pred annotation provided by ANNOVAR"> +##INFO=<ID=RadialSVM_score,Number=.,Type=String,Description="RadialSVM_score annotation provided by ANNOVAR"> +##INFO=<ID=RadialSVM_pred,Number=.,Type=String,Description="RadialSVM_pred annotation provided by ANNOVAR"> +##INFO=<ID=LR_score,Number=.,Type=String,Description="LR_score annotation provided by ANNOVAR"> +##INFO=<ID=LR_pred,Number=.,Type=String,Description="LR_pred annotation provided by ANNOVAR"> +##INFO=<ID=VEST3_score,Number=.,Type=String,Description="VEST3_score annotation provided by ANNOVAR"> +##INFO=<ID=CADD_raw,Number=.,Type=String,Description="CADD_raw annotation provided by ANNOVAR"> +##INFO=<ID=CADD_phred,Number=.,Type=String,Description="CADD_phred annotation provided by ANNOVAR"> +##INFO=<ID=GERP++_RS,Number=.,Type=String,Description="GERP++_RS annotation provided by ANNOVAR"> +##INFO=<ID=phyloP46way_placental,Number=.,Type=String,Description="phyloP46way_placental annotation provided by ANNOVAR"> +##INFO=<ID=phyloP100way_vertebrate,Number=.,Type=String,Description="phyloP100way_vertebrate annotation provided by ANNOVAR"> +##INFO=<ID=SiPhy_29way_logOdds,Number=.,Type=String,Description="SiPhy_29way_logOdds annotation provided by ANNOVAR"> +##INFO=<ID=CLNALLELEID,Number=.,Type=String,Description="CLNALLELEID annotation provided by ANNOVAR"> +##INFO=<ID=ALLELE_END,Number=0,Type=Flag,Description="Flag the end of ANNOVAR annotation for one alternative allele"> +##bcftools_filterCommand=filter --include 'INFO/LOF != "." | INFO/CLNSIG != "." | INFO/cosmic70 != "." | INFO/Polyphen2_HDIV_pred != "." | INFO/LRT_pred != "." | INFO/MutationTaster_pred != "." | INFO/MutationAssessor_pred != "." | INFO/FATHMM_pred != "."' --output-type v --threads 1 input.vcf.gz; Date=Wed Sep 7 20:55:15 2022 +##SnpEffCmd="SnpEff -i vcf -o vcf -stats /home/galaxy/galaxy/database/datasets/001/336/dataset_1336200.dat hg38 /home/galaxy/galaxy/database/datasets/001/336/dataset_1336198.dat " +##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' "> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 01002_normal 01002_tumor +chr1 42536528 . AAG A . MinMMQSdiff DP=160;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10106;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=ID\x3dCOSM391243\x3bOCCURENCE\x3d1(lung),1(pancreas),4(large_intestine);SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=A|frameshift_variant|HIGH|CCDC30|CCDC30|transcript|NM_001080850.2|protein_coding|2/16|c.60_61delGA|p.Lys21fs|170/3098|60/2352|20/783||INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR 0/0:.:50:50,0:26,0:24,0 0/1:.:110:104,6:56,2:48,4 +chr1 100206310 . TA T . MinMMQSdiff DP=144;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.1157;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=433480;CLNDN=Maple_syrup_urine_disease|not_specified;CLNDISDB=MONDO:MONDO:0009563,MeSH:D008375,MedGen:C0024776,OMIM:248600,OMIM:PS248600,Orphanet:ORPHA511,SNOMED_CT:27718001|MedGen:CN169374;CLNREVSTAT=criteria_provided,_multiple_submitters,_no_conflicts;CLNSIG=Benign;ALLELE_END;ANN=T|intron_variant|MODIFIER|DBT|DBT|transcript|NM_001918.3|protein_coding|9/10|c.1210-10delT|||||| GT:GQ:DP:AD:ADF:ADR 0/0:.:42:40,0:23,0:17,0 0/1:.:102:89,6:54,3:35,3 +chr1 100539628 . T C . PASS DP=18;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.068627;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.77;SIFT_pred=T;Polyphen2_HDIV_score=0.386;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.157;Polyphen2_HVAR_pred=B;LRT_score=0.119;LRT_pred=U;MutationTaster_score=0.982;MutationTaster_pred=N;MutationAssessor_score=0;MutationAssessor_pred=N;FATHMM_score=1.27;FATHMM_pred=T;RadialSVM_score=-0.979;RadialSVM_pred=T;LR_score=0.014;LR_pred=T;VEST3_score=0.371;CADD_raw=-1.497;CADD_phred=0.017;GERP++_RS=2.92;phyloP46way_placental=1.237;phyloP100way_vertebrate=1.470;SiPhy_29way_logOdds=8.418;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|GPR88|GPR88|transcript|NM_022049.2|protein_coding|2/2|c.662T>C|p.Val221Ala|1066/3465|662/1155|221/384|| GT:GQ:DP:AD:ADF:ADR 0/0:.:10:10,0:8,0:2,0 0/1:.:8:5,3:0,0:5,3 +chr1 112912805 . TA T . PASS DP=142;SOMATIC;SS=2;SSC=14;GPV=1;SPV=0.039564;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=276120;CLNDN=Hyperinsulinism,_Dominant;CLNDISDB=MedGen:CN239341;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Uncertain_significance;ALLELE_END;ANN=T|3_prime_UTR_variant|MODIFIER|SLC16A1|SLC16A1|transcript|NM_001166496.1|protein_coding|5/5|c.*1085delT|||||1085|,T|3_prime_UTR_variant|MODIFIER|SLC16A1|SLC16A1|transcript|NM_003051.3|protein_coding|5/5|c.*1085delT|||||1085| GT:GQ:DP:AD:ADF:ADR 0/0:.:43:43,0:22,0:21,0 0/1:.:99:82,8:45,7:37,1 +chr1 151088217 . T G . PASS DP=134;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11875;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.01;SIFT_pred=D;Polyphen2_HDIV_score=0.999;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.977;Polyphen2_HVAR_pred=D;LRT_score=0.000;LRT_pred=D;MutationTaster_score=0.996;MutationTaster_pred=D;MutationAssessor_score=2.48;MutationAssessor_pred=M;FATHMM_score=-0.17;FATHMM_pred=T;RadialSVM_score=-0.479;RadialSVM_pred=T;LR_score=0.294;LR_pred=T;VEST3_score=0.897;CADD_raw=4.062;CADD_phred=20.9;GERP++_RS=0.551;phyloP46way_placental=0.181;phyloP100way_vertebrate=0.031;SiPhy_29way_logOdds=9.216;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_001323910.1|protein_coding|2/10|c.28T>G|p.Leu10Val|385/2027|28/1395|10/464||,G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_001323907.1|protein_coding|2/8|c.28T>G|p.Leu10Val|385/1745|28/1113|10/370||,G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_001323908.1|protein_coding|2/9|c.28T>G|p.Leu10Val|417/2011|28/1347|10/448||,G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_001323909.1|protein_coding|2/8|c.28T>G|p.Leu10Val|385/1865|28/1233|10/410||,G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_001323912.1|protein_coding|3/8|c.28T>G|p.Leu10Val|504/1816|28/1065|10/354||,G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_001323913.1|protein_coding|2/8|c.28T>G|p.Leu10Val|385/1811|28/1179|10/392||,G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_001323906.1|protein_coding|2/10|c.28T>G|p.Leu10Val|385/2946|28/1359|10/452||,G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_001323911.1|protein_coding|2/9|c.28T>G|p.Leu10Val|385/2832|28/1245|10/414||,G|missense_variant|MODERATE|GABPB2|GABPB2|transcript|NM_144618.2|protein_coding|2/9|c.28T>G|p.Leu10Val|359/1953|28/1347|10/448|| GT:GQ:DP:AD:ADF:ADR 0/0:.:39:39,0:18,0:21,0 0/1:.:95:88,6:48,5:40,1 +chr1 193251844 . G GT . MinMMQSdiff DP=181;SOMATIC;SS=2;SSC=14;GPV=1;SPV=0.039165;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=279150;CLNDN=Parathyroid_carcinoma|Hyperparathyroidism_2|Isolated_Hyperparathyroidism;CLNDISDB=Human_Phenotype_Ontology:HP:0006780,MONDO:MONDO:0012004,MedGen:C0687150,OMIM:608266,Orphanet:ORPHA143,SNOMED_CT:255037004|MONDO:MONDO:0007768,MedGen:C1704981,OMIM:145001,Orphanet:ORPHA99880|MedGen:CN239442;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Uncertain_significance;ALLELE_END;ANN=GT|3_prime_UTR_variant|MODIFIER|CDC73|CDC73|transcript|NM_024529.4|protein_coding|17/17|c.*1144dupT|||||1145|INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR 0/0:.:49:48,0:23,0:25,0 0/1:.:132:120,10:60,4:60,6 +chr1 197090091 . G GA . MinMMQSdiff DP=139;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.073566;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=193063;CLNDN=not_provided;CLNDISDB=MedGen:CN517202;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Uncertain_significance;ALLELE_END;ANN=GA|splice_region_variant&intron_variant|LOW|ASPM|ASPM|transcript|NM_018136.4|protein_coding|24/27|c.9830-8dupT||||||,GA|splice_region_variant&intron_variant|LOW|ASPM|ASPM|transcript|NM_001206846.1|protein_coding|23/26|c.5075-8dupT|||||| GT:GQ:DP:AD:ADF:ADR 0/0:.:42:42,0:22,0:20,0 0/1:.:97:89,7:56,5:33,2 +chr1 215741541 . G GA . MinMMQSdiff DP=159;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.09137;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=195468;CLNDN=not_specified;CLNDISDB=MedGen:CN169374;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;ALLELE_END;ANN=GA|splice_region_variant&intron_variant|LOW|USH2A|USH2A|transcript|NM_206933.2|protein_coding|59/71|c.11549-5dupT|||||| GT:GQ:DP:AD:ADF:ADR 0/0:.:46:44,0:20,0:24,0 0/1:.:113:104,7:59,3:45,4 +chr1 247949492 rs200574966 G C . MinMMQSdiff DP=58;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.076494;FREQ=ExAC:0.9999,.,9.101e-05|GnomAD_exomes:1,.,1.196e-05|KOREAN:0.9798,.,0.02019|TOMMO:0.9837,.,0.01629|dbGaP_PopFreq:0.9983,0,0.001659;GENEINFO=OR2L13:284521|OR2L8:391190;INT;NSM;R5;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.11;SIFT_pred=T;Polyphen2_HDIV_score=0.001;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.021;Polyphen2_HVAR_pred=B;LRT_score=0.447;LRT_pred=U;MutationTaster_score=1.000;MutationTaster_pred=N;MutationAssessor_score=-0.13;MutationAssessor_pred=N;FATHMM_score=1.28;FATHMM_pred=T;RadialSVM_score=-1.057;RadialSVM_pred=T;LR_score=0.035;LR_pred=T;VEST3_score=0.097;CADD_raw=-1.748;CADD_phred=0.010;GERP++_RS=-3.61;phyloP46way_placental=-1.273;phyloP100way_vertebrate=-1.473;SiPhy_29way_logOdds=5.646;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|OR2L8|OR2L8|transcript|NM_001001963.1|protein_coding|1/1|c.635G>C|p.Gly212Ala|635/939|635/939|212/312||,C|intron_variant|MODIFIER|OR2L13|OR2L13|transcript|NM_001304535.1|protein_coding|1/1|c.-19+12108G>C||||||,C|intron_variant|MODIFIER|OR2L13|OR2L13|transcript|NM_175911.3|protein_coding|1/2|c.-144+12108G>C|||||| GT:GQ:DP:AD:ADF:ADR 0/0:.:11:11,0:6,0:5,0 0/1:.:47:36,11:23,3:13,8 +chr2 43819994 rs200839584 C T . PASS DP=162;SOMATIC;SS=2;SSC=94;GPV=1;SPV=3.2187e-10;CLNACC=.,RCV000310689.2|RCV001143371.1;CLNDISDB=.,MedGen:CN517202|GeneReviews:NBK131810/MONDO:MONDO:0020747/MedGen:C5231390/OMIM:210250;CLNDN=.,not_provided|Sitosterolemia_1;CLNORIGIN=.,1;CLNREVSTAT=.,single|single;CLNSIG=.,0|0;CLNVI=.,Illumina_Clinical_Services_Laboratory\x2cIllumina:764360;FREQ=1000Genomes:0.9996,0.0003994|ExAC:0.9999,9.887e-05|GnomAD:1,4.28e-05|GnomAD_exomes:0.9999,0.0001074|PAGE_STUDY:0.9998,0.0001652|TOPMED:0.9999,6.8e-05|dbGaP_PopFreq:0.9999,7.061e-05;GENEINFO=DYNC2LI1:51626|ABCG5:64240;INT;NSM;R3;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.33;SIFT_pred=T;Polyphen2_HDIV_score=0.279;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.04;Polyphen2_HVAR_pred=B;LRT_score=0.078;LRT_pred=N;MutationTaster_score=0.997;MutationTaster_pred=N;MutationAssessor_score=1.375;MutationAssessor_pred=L;FATHMM_score=-0.63;FATHMM_pred=T;RadialSVM_score=-0.980;RadialSVM_pred=T;LR_score=0.189;LR_pred=T;VEST3_score=0.114;CADD_raw=-0.627;CADD_phred=1.219;GERP++_RS=-2.75;phyloP46way_placental=-0.921;phyloP100way_vertebrate=0.120;SiPhy_29way_logOdds=12.741;CLNALLELEID=268994;CLNDN=Sitosterolemia_1|not_provided;CLNDISDB=MONDO:MONDO:0020747,MedGen:C5231390,OMIM:210250|MedGen:CN517202;CLNREVSTAT=criteria_provided,_multiple_submitters,_no_conflicts;CLNSIG=Uncertain_significance;ALLELE_END;ANN=T|missense_variant|MODERATE|ABCG5|ABCG5|transcript|NM_022436.2|protein_coding|11/13|c.1570G>A|p.Val524Ile|1710/2740|1570/1956|524/651|| GT:GQ:DP:AD:ADF:ADR 0/0:.:48:48,0:27,0:21,0 0/1:.:114:64,50:32,33:32,17 +chr2 47805601 . AT A . MinMMQSdiff DP=126;SOMATIC;SS=2;SSC=16;GPV=1;SPV=0.025068;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=94891;CLNDN=Hereditary_nonpolyposis_colorectal_cancer_type_5|Hereditary_cancer-predisposing_syndrome|not_specified|not_provided;CLNDISDB=MONDO:MONDO:0013710,MedGen:C1833477,OMIM:614350|MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202;CLNREVSTAT=criteria_provided,_multiple_submitters,_no_conflicts;CLNSIG=Benign/Likely_benign;ALLELE_END;ANN=A|splice_region_variant&intron_variant|LOW|MSH6|MSH6|transcript|NM_000179.2|protein_coding|6/9|c.3557-4delT||||||INFO_REALIGN_3_PRIME,A|splice_region_variant&intron_variant|LOW|MSH6|MSH6|transcript|NM_001281492.1|protein_coding|4/7|c.3167-4delT||||||INFO_REALIGN_3_PRIME,A|splice_region_variant&intron_variant|LOW|MSH6|MSH6|transcript|NM_001281493.1|protein_coding|5/8|c.2651-4delT||||||INFO_REALIGN_3_PRIME,A|splice_region_variant&intron_variant|LOW|MSH6|MSH6|transcript|NM_001281494.1|protein_coding|6/9|c.2651-4delT||||||INFO_REALIGN_3_PRIME,A|downstream_gene_variant|MODIFIER|FBXO11|FBXO11|transcript|NM_001190274.1|protein_coding||c.*2516delA|||||1318|,A|downstream_gene_variant|MODIFIER|FBXO11|FBXO11|transcript|NM_025133.4|protein_coding||c.*2516delA|||||1318| GT:GQ:DP:AD:ADF:ADR 0/0:.:35:33,0:19,0:14,0 0/1:.:91:77,11:44,6:33,5 +chr2 165953651 . G GCCCGCTCACCCGCTCA . MinMMQSdiff DP=49;SOMATIC;SS=2;SSC=17;GPV=1;SPV=0.018691;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=405364;CLNDN=not_specified;CLNDISDB=MedGen:CN169374;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Likely_benign;ALLELE_END;ANN=GCCCGCTCACCCGCTCA|upstream_gene_variant|MODIFIER|LOC102724058|LOC102724058|transcript|NR_110598.1|pseudogene||n.-3767_-3766insCCCGCTCACCCGCTCA|||||3766|,GCCCGCTCACCCGCTCA|intron_variant|MODIFIER|TTC21B|TTC21B|transcript|NM_024753.4|protein_coding|1/28|c.21+18_21+33dupTGAGCGGGTGAGCGGG|||||| GT:GQ:DP:AD:ADF:ADR 0/0:.:11:6,1:5,0:1,1 0/1:.:38:7,15:5,6:2,9 +chr4 2898230 . T C . PASS DP=150;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.048075;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0;SIFT_pred=D;Polyphen2_HDIV_score=1.0;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=1.0;Polyphen2_HVAR_pred=D;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=1.75;MutationAssessor_pred=L;FATHMM_score=0.82;FATHMM_pred=T;RadialSVM_score=-0.555;RadialSVM_pred=T;LR_score=0.270;LR_pred=T;VEST3_score=0.978;CADD_raw=4.849;CADD_phred=27.6;GERP++_RS=5.86;phyloP46way_placental=2.235;phyloP100way_vertebrate=7.975;SiPhy_29way_logOdds=16.256;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|ADD1|ADD1|transcript|NM_014189.3|protein_coding|7/15|c.788T>C|p.Leu263Pro|976/4047|788/2307|263/768||,C|missense_variant|MODERATE|ADD1|ADD1|transcript|NM_001119.4|protein_coding|7/15|c.788T>C|p.Leu263Pro|976/3954|788/2214|263/737||,C|missense_variant|MODERATE|ADD1|ADD1|transcript|NM_014190.3|protein_coding|7/16|c.788T>C|p.Leu263Pro|976/3988|788/1896|263/631||,C|missense_variant|MODERATE|ADD1|ADD1|transcript|NM_176801.2|protein_coding|7/16|c.788T>C|p.Leu263Pro|976/4081|788/1989|263/662||,C|missense_variant|MODERATE|ADD1|ADD1|transcript|NM_001286645.1|protein_coding|8/18|c.788T>C|p.Leu263Pro|1651/4756|788/1989|263/662|| GT:GQ:DP:AD:ADF:ADR 0/0:.:52:51,0:20,0:31,0 0/1:.:98:90,7:25,6:65,1 +chr5 38476522 . C CT . PASS DP=153;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11056;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=297531;CLNDN=Stüve-Wiedemann_syndrome;CLNDISDB=MONDO:MONDO:0011108,MedGen:C0796176,OMIM:601559,Orphanet:ORPHA3206;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;ALLELE_END;ANN=CT|3_prime_UTR_variant|MODIFIER|LIFR|LIFR|transcript|NM_001127671.1|protein_coding|20/20|c.*5072dupA|||||5072|,CT|3_prime_UTR_variant|MODIFIER|LIFR|LIFR|transcript|NM_002310.5|protein_coding|20/20|c.*5072dupA|||||5072| GT:GQ:DP:AD:ADF:ADR 0/0:.:48:45,0:22,0:23,0 0/1:.:105:98,6:60,3:38,3 +chr5 112775612 . TA T . PASS DP=161;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.042342;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=180169;CLNDN=Hereditary_cancer-predisposing_syndrome|not_specified|not_provided;CLNDISDB=MONDO:MONDO:0015356,MedGen:C0027672,Orphanet:ORPHA140162,SNOMED_CT:699346009|MedGen:CN169374|MedGen:CN517202;CLNREVSTAT=criteria_provided,_multiple_submitters,_no_conflicts;CLNSIG=Benign/Likely_benign;ALLELE_END;ANN=T|splice_region_variant&intron_variant|LOW|APC|APC|transcript|NM_000038.5|protein_coding|4/15|c.423-4delA||||||INFO_REALIGN_3_PRIME,T|splice_region_variant&intron_variant|LOW|APC|APC|transcript|NM_001127511.2|protein_coding|3/13|c.453-4delA||||||INFO_REALIGN_3_PRIME,T|splice_region_variant&intron_variant|LOW|APC|APC|transcript|NM_001127510.2|protein_coding|5/16|c.423-4delA||||||INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR 0/0:.:47:46,1:24,1:22,0 0/1:.:114:98,13:52,7:46,6 +chr5 141527699 . TA T . MinMMQSdiff DP=123;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.039946;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=501019;CLNDN=not_specified;CLNDISDB=MedGen:CN169374;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;ALLELE_END;ANN=T|splice_region_variant&intron_variant|LOW|DIAPH1|DIAPH1|transcript|NM_005219.4|protein_coding|23/27|c.3149-3delT||||||,T|splice_region_variant&intron_variant|LOW|DIAPH1|DIAPH1|transcript|NM_001079812.2|protein_coding|22/26|c.3122-3delT||||||,T|splice_region_variant&intron_variant|LOW|DIAPH1|DIAPH1|transcript|NM_001314007.1|protein_coding|23/28|c.3149-3delT|||||| GT:GQ:DP:AD:ADF:ADR 0/0:.:34:22,1:12,1:10,0 0/1:.:89:59,17:31,7:28,10 +chr6 13364935 rs1407685850 A C . PASS DP=73;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.078592;FREQ=GnomAD:1,.,7.13e-06|TOMMO:0.9993,0.0006563,.|TOPMED:1,.,3.778e-06|dbGaP_PopFreq:0.9999,.,7.117e-05;GENEINFO=GFOD1:54438;NSM;R3;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=1;SIFT_pred=T;Polyphen2_HDIV_score=0.902;Polyphen2_HDIV_pred=P;Polyphen2_HVAR_score=0.468;Polyphen2_HVAR_pred=P;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=1.32;MutationAssessor_pred=L;FATHMM_score=1.6;FATHMM_pred=T;RadialSVM_score=-1.023;RadialSVM_pred=T;LR_score=0.037;LR_pred=T;VEST3_score=0.42;CADD_raw=2.989;CADD_phred=15.97;GERP++_RS=1.29;phyloP46way_placental=0.058;phyloP100way_vertebrate=-0.523;SiPhy_29way_logOdds=11.050;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|GFOD1|GFOD1|transcript|NM_018988.3|protein_coding|2/2|c.981T>G|p.Asp327Glu|1728/3308|981/1173|327/390||,C|missense_variant|MODERATE|GFOD1|GFOD1|transcript|NM_001242630.1|protein_coding|2/2|c.672T>G|p.Asp224Glu|956/2536|672/864|224/287||,C|missense_variant|MODERATE|GFOD1|GFOD1|transcript|NM_001242628.1|protein_coding|2/2|c.672T>G|p.Asp224Glu|901/2481|672/864|224/287|| GT:GQ:DP:AD:ADF:ADR 0/0:.:21:21,0:6,0:15,0 0/1:.:52:44,7:17,6:27,1 +chr6 47878370 rs746678221 C T . PASS DP=178;SOMATIC;SS=2;SSC=88;GPV=1;SPV=1.5004e-09;FREQ=ExAC:1,1.68e-05|GnomAD:1,1.428e-05|GnomAD_exomes:1,2.007e-05|TOPMED:1,1.889e-05|dbGaP_PopFreq:1,4.341e-05;GENEINFO=PTCHD4:442213;NSM;R3;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.57;SIFT_pred=T;Polyphen2_HDIV_score=0.105;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.005;Polyphen2_HVAR_pred=B;LRT_score=0.001;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=0;MutationAssessor_pred=N;FATHMM_score=-2.95;FATHMM_pred=D;RadialSVM_score=-0.486;RadialSVM_pred=T;LR_score=0.343;LR_pred=T;VEST3_score=0.375;CADD_raw=2.859;CADD_phred=15.52;GERP++_RS=5.29;phyloP46way_placental=1.612;phyloP100way_vertebrate=4.614;SiPhy_29way_logOdds=15.443;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=T|missense_variant|MODERATE|PTCHD4|PTCHD4|transcript|NM_001013732.3|protein_coding|3/3|c.2474G>A|p.Arg825Gln|2508/2850|2474/2541|825/846|| GT:GQ:DP:AD:ADF:ADR 0/0:.:46:46,0:18,0:28,0 0/1:.:132:77,55:38,30:39,25 +chr7 103149391 rs1813278496 T C . PASS DP=37;SOMATIC;SS=2;SSC=12;GPV=1;SPV=0.057896;FREQ=TOMMO:0.9981,0.00191;GENEINFO=NAPEPLD:222236|LOC105375434:105375434;INT;NSM;R5;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.82;SIFT_pred=T;Polyphen2_HDIV_score=0.0;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.0;Polyphen2_HVAR_pred=B;LRT_score=.;LRT_pred=.;MutationTaster_score=1.000;MutationTaster_pred=N;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=1.34;FATHMM_pred=T;RadialSVM_score=-0.990;RadialSVM_pred=T;LR_score=0.034;LR_pred=T;VEST3_score=0.019;CADD_raw=-0.828;CADD_phred=0.604;GERP++_RS=0.629;phyloP46way_placental=0.144;phyloP100way_vertebrate=-0.534;SiPhy_29way_logOdds=4.841;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|upstream_gene_variant|MODIFIER|NAPEPLD|NAPEPLD|transcript|NM_001122838.1|protein_coding||c.-20615A>G|||||269|,C|upstream_gene_variant|MODIFIER|NAPEPLD|NAPEPLD|transcript|NM_198990.4|protein_coding||c.-20615A>G|||||269|,C|intergenic_region|MODIFIER|NAPEPLD-DPY19L2P2|NAPEPLD-DPY19L2P2|intergenic_region|NAPEPLD-DPY19L2P2|||n.103149391T>C|||||| GT:GQ:DP:AD:ADF:ADR 0/0:.:13:13,0:5,0:8,0 0/1:.:24:18,6:4,4:14,2 +chr7 107202971 . AT A . MinMMQSdiff DP=172;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.043842;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=301392;CLNDN=Congenital_disorder_of_glycosylation;CLNDISDB=MONDO:MONDO:0015286,MedGen:C0282577,OMIM:PS212065,Orphanet:ORPHA137,SNOMED_CT:238049009;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Likely_benign;ALLELE_END;ANN=A|3_prime_UTR_variant|MODIFIER|COG5|COG5|transcript|NM_006348.3|protein_coding|22/22|c.*544delA|||||544|,A|3_prime_UTR_variant|MODIFIER|COG5|COG5|transcript|NM_181733.2|protein_coding|21/21|c.*544delA|||||544|,A|downstream_gene_variant|MODIFIER|HBP1|HBP1|transcript|NM_001244262.1|protein_coding||c.*1541delT|||||443|,A|downstream_gene_variant|MODIFIER|HBP1|HBP1|transcript|NM_012257.3|protein_coding||c.*1541delT|||||443|,A|downstream_gene_variant|MODIFIER|COG5|COG5|transcript|NM_001161520.1|protein_coding||c.*7550delA|||||4881| GT:GQ:DP:AD:ADF:ADR 0/0:.:38:37,1:27,0:10,1 0/1:.:134:107,17:60,13:47,4 +chr8 31076300 . CT C . MinMMQSdiff DP=172;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.087593;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=790795;CLNDN=Werner_syndrome;CLNDISDB=MONDO:MONDO:0010196,MedGen:C0043119,OMIM:277700,Orphanet:ORPHA902,SNOMED_CT:51626007;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;ALLELE_END;ANN=C|intron_variant|MODIFIER|WRN|WRN|transcript|NM_000553.4|protein_coding|8/34|c.839+25delT||||||INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR 0/0:.:50:47,0:24,0:23,0 0/1:.:122:109,7:61,5:48,2 +chr8 80687384 rs1585953247 T C . PASS DP=63;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.094475;FREQ=Korea1K:1,0,.|TOPMED:1,.,3.778e-06|dbGaP_PopFreq:1,.,0;GENEINFO=ZNF704:619279;NSM;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.39;SIFT_pred=T;Polyphen2_HDIV_score=0.143;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.143;Polyphen2_HVAR_pred=B;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=2.08;MutationAssessor_pred=M;FATHMM_score=1.55;FATHMM_pred=T;RadialSVM_score=-1.053;RadialSVM_pred=T;LR_score=0.097;LR_pred=T;VEST3_score=0.34;CADD_raw=3.183;CADD_phred=16.65;GERP++_RS=5.7;phyloP46way_placental=2.173;phyloP100way_vertebrate=4.803;SiPhy_29way_logOdds=15.974;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|ZNF704|ZNF704|transcript|NM_001033723.2|protein_coding|4/9|c.400A>G|p.Ser134Gly|632/14386|400/1239|134/412|| GT:GQ:DP:AD:ADF:ADR 0/0:.:19:19,0:8,0:11,0 0/1:.:44:36,6:19,3:17,3 +chr9 85956346 . C CT . PASS DP=182;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10506;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=CT|splice_acceptor_variant&intron_variant|HIGH|NAA35|NAA35|transcript|NM_001321881.1|protein_coding|2/22|c.125-3dupT||||||INFO_REALIGN_3_PRIME,CT|splice_acceptor_variant&intron_variant|HIGH|NAA35|NAA35|transcript|NM_024635.3|protein_coding|2/22|c.125-3dupT||||||INFO_REALIGN_3_PRIME,CT|splice_acceptor_variant&intron_variant|HIGH|NAA35|NAA35|transcript|NM_001321882.1|protein_coding|2/22|c.125-3dupT||||||INFO_REALIGN_3_PRIME;LOF=(NAA35|NAA35|3|1.00) GT:GQ:DP:AD:ADF:ADR 0/0:.:56:54,0:38,0:16,0 0/1:.:126:115,6:67,5:48,1 +chr9 112574594 . C T . PASS DP=124;SOMATIC;SS=2;SSC=18;GPV=1;SPV=0.01311;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0;SIFT_pred=D;Polyphen2_HDIV_score=1.0;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.996;Polyphen2_HVAR_pred=D;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=0.695;MutationAssessor_pred=N;FATHMM_score=0.96;FATHMM_pred=T;RadialSVM_score=-0.785;RadialSVM_pred=T;LR_score=0.190;LR_pred=T;VEST3_score=0.829;CADD_raw=3.837;CADD_phred=19.49;GERP++_RS=6.07;phyloP46way_placental=2.884;phyloP100way_vertebrate=4.349;SiPhy_29way_logOdds=20.644;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=T|missense_variant|MODERATE|KIAA1958|KIAA1958|transcript|NM_001287036.1|protein_coding|2/5|c.514C>T|p.Arg172Cys|689/7652|514/2235|172/744||,T|missense_variant|MODERATE|KIAA1958|KIAA1958|transcript|NM_001287038.1|protein_coding|2/4|c.514C>T|p.Arg172Cys|689/7558|514/1347|172/448||,T|missense_variant|MODERATE|KIAA1958|KIAA1958|transcript|NM_133465.3|protein_coding|2/4|c.514C>T|p.Arg172Cys|689/7568|514/2151|172/716|| GT:GQ:DP:AD:ADF:ADR 0/0:.:42:42,0:13,0:29,0 0/1:.:82:72,10:39,4:33,6 +chr9 127651572 . CCT C . MinMMQSdiff DP=149;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10418;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=202275;CLNDN=not_specified;CLNDISDB=MedGen:CN169374;CLNREVSTAT=criteria_provided,_multiple_submitters,_no_conflicts;CLNSIG=Benign;ALLELE_END;ANN=C|intron_variant|MODIFIER|STXBP1|STXBP1|transcript|NM_003165.3|protein_coding|1/19|c.38-16_38-15delCT||||||INFO_REALIGN_3_PRIME,C|intron_variant|MODIFIER|STXBP1|STXBP1|transcript|NM_001032221.3|protein_coding|1/18|c.38-16_38-15delCT||||||INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR 0/0:.:46:46,0:30,0:16,0 0/1:.:103:97,6:53,3:44,3 +chr9 130664691 . T C . PASS DP=51;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11761;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.04;SIFT_pred=D;Polyphen2_HDIV_score=0.009;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.005;Polyphen2_HVAR_pred=B;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=0.695;MutationAssessor_pred=N;FATHMM_score=2.56;FATHMM_pred=T;RadialSVM_score=-1.060;RadialSVM_pred=T;LR_score=0.022;LR_pred=T;VEST3_score=0.912;CADD_raw=2.439;CADD_phred=14.11;GERP++_RS=3.23;phyloP46way_placental=1.594;phyloP100way_vertebrate=7.058;SiPhy_29way_logOdds=8.170;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|PRDM12|PRDM12|transcript|NM_021619.2|protein_coding|1/5|c.38T>C|p.Leu13Pro|98/2492|38/1104|13/367|| GT:GQ:DP:AD:ADF:ADR 0/0:.:16:16,0:12,0:4,0 0/1:.:35:27,5:18,1:9,4 +chr10 87965536 . CT C . PASS DP=175;SOMATIC;SS=2;SSC=17;GPV=1;SPV=0.01923;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=240890;CLNDN=PTEN_hamartoma_tumor_syndrome;CLNDISDB=MONDO:MONDO:0017623,MedGen:C1959582,OMIM:601728,Orphanet:ORPHA306498;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;ALLELE_END;ANN=C|3_prime_UTR_variant|MODIFIER|PTEN|PTEN|transcript|NM_001304717.2|protein_coding|10/10|c.*75delT|||||75|INFO_REALIGN_3_PRIME,C|3_prime_UTR_variant|MODIFIER|PTEN|PTEN|transcript|NM_000314.6|protein_coding|9/9|c.*75delT|||||75|INFO_REALIGN_3_PRIME,C|3_prime_UTR_variant|MODIFIER|PTEN|PTEN|transcript|NM_001304718.1|protein_coding|9/9|c.*75delT|||||75|INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR 0/0:.:55:54,0:30,0:24,0 0/1:.:120:106,10:66,9:40,1 +chr11 62786683 rs2084280733 T C . PASS DP=52;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.040211;FREQ=TOMMO:0.9989,0.001074;GENEINFO=TAF6L:10629|TMEM179B:374395;NSM;R5;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.09;SIFT_pred=T;Polyphen2_HDIV_score=0.0;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.001;Polyphen2_HVAR_pred=B;LRT_score=0.071;LRT_pred=N;MutationTaster_score=0.999;MutationTaster_pred=N;MutationAssessor_score=0.345;MutationAssessor_pred=N;FATHMM_score=0.88;FATHMM_pred=T;RadialSVM_score=-1.057;RadialSVM_pred=T;LR_score=0.051;LR_pred=T;VEST3_score=0.314;CADD_raw=0.607;CADD_phred=7.271;GERP++_RS=1.57;phyloP46way_placental=0.485;phyloP100way_vertebrate=1.378;SiPhy_29way_logOdds=4.335;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|TAF6L|TAF6L|transcript|NM_006473.3|protein_coding|11/11|c.1256T>C|p.Leu419Pro|1457/2115|1256/1869|419/622||,C|upstream_gene_variant|MODIFIER|TMEM179B|TMEM179B|transcript|NM_199337.2|protein_coding||c.-749T>C|||||719|,C|upstream_gene_variant|MODIFIER|MIR6748|MIR6748|transcript|NR_106806.1|pseudogene||n.-3132T>C|||||3132|,C|downstream_gene_variant|MODIFIER|TMEM223|TMEM223|transcript|NM_001080501.2|protein_coding||c.*3940A>G|||||3632| GT:GQ:DP:AD:ADF:ADR 0/0:.:16:16,0:9,0:7,0 0/1:.:36:28,8:16,1:12,7 +chr12 52601418 . T C . PASS DP=87;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10996;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=1;SIFT_pred=T;Polyphen2_HDIV_score=0.212;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.055;Polyphen2_HVAR_pred=B;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=-0.46;MutationAssessor_pred=N;FATHMM_score=-1.52;FATHMM_pred=D;RadialSVM_score=-0.798;RadialSVM_pred=T;LR_score=0.191;LR_pred=T;VEST3_score=0.351;CADD_raw=0.738;CADD_phred=7.920;GERP++_RS=3.26;phyloP46way_placental=1.025;phyloP100way_vertebrate=-0.187;SiPhy_29way_logOdds=8.397;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|KRT72|KRT72|transcript|NM_001146225.1|protein_coding|1/10|c.35A>G|p.Glu12Gly|121/1888|35/1536|12/511||,C|missense_variant|MODERATE|KRT72|KRT72|transcript|NM_001146226.1|protein_coding|1/8|c.35A>G|p.Glu12Gly|121/1889|35/1410|12/469||,C|missense_variant|MODERATE|KRT72|KRT72|transcript|NM_080747.2|protein_coding|1/9|c.35A>G|p.Glu12Gly|121/2015|35/1536|12/511|| GT:GQ:DP:AD:ADF:ADR 0/0:.:26:26,0:17,0:9,0 0/1:.:61:55,6:40,5:15,1 +chr12 53467852 . TA T . PASS DP=136;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10327;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=ID\x3dCOSM1606323\x3bOCCURENCE\x3d1(liver);SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=T|downstream_gene_variant|MODIFIER|PCBP2-OT1|PCBP2-OT1|transcript|NR_109828.1|pseudogene||n.*2796delA|||||2796|,T|intron_variant|MODIFIER|PCBP2|PCBP2|transcript|NM_005016.5|protein_coding|12/14|c.838+22delA||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|PCBP2|PCBP2|transcript|NM_001098620.2|protein_coding|11/13|c.733+22delA||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|PCBP2|PCBP2|transcript|NM_001128911.1|protein_coding|12/14|c.838+22delA||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|PCBP2|PCBP2|transcript|NM_001128912.1|protein_coding|12/14|c.826+22delA||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|PCBP2|PCBP2|transcript|NM_001128913.1|protein_coding|11/13|c.745+22delA||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|PCBP2|PCBP2|transcript|NM_001128914.1|protein_coding|10/12|c.694+572delA||||||INFO_REALIGN_3_PRIME,T|intron_variant|MODIFIER|PCBP2|PCBP2|transcript|NM_031989.4|protein_coding|12/14|c.826+22delA||||||INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR 0/0:.:38:36,0:18,0:18,0 0/1:.:98:90,7:39,3:51,4 +chr12 75207331 . A G . PASS DP=78;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10007;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0;SIFT_pred=D;Polyphen2_HDIV_score=1.0;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.993;Polyphen2_HVAR_pred=D;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=3.105;MutationAssessor_pred=M;FATHMM_score=-4.78;FATHMM_pred=D;RadialSVM_score=1.096;RadialSVM_pred=D;LR_score=0.966;LR_pred=D;VEST3_score=0.989;CADD_raw=4.158;CADD_phred=21.5;GERP++_RS=4.44;phyloP46way_placental=1.973;phyloP100way_vertebrate=8.932;SiPhy_29way_logOdds=14.145;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=G|missense_variant|MODERATE|KCNC2|KCNC2|transcript|NM_139137.3|protein_coding|2/5|c.653T>C|p.Leu218Pro|1214/5505|653/1917|218/638||,G|missense_variant|MODERATE|KCNC2|KCNC2|transcript|NM_001260497.1|protein_coding|2/5|c.653T>C|p.Leu218Pro|1214/6077|653/1857|218/618||,G|missense_variant|MODERATE|KCNC2|KCNC2|transcript|NM_001260498.1|protein_coding|2/5|c.653T>C|p.Leu218Pro|1214/3470|653/1890|218/629||,G|missense_variant|MODERATE|KCNC2|KCNC2|transcript|NM_001260499.1|protein_coding|2/4|c.653T>C|p.Leu218Pro|1214/5340|653/1752|218/583||,G|missense_variant|MODERATE|KCNC2|KCNC2|transcript|NM_139136.3|protein_coding|2/6|c.653T>C|p.Leu218Pro|1214/3565|653/1842|218/613||,G|missense_variant|MODERATE|KCNC2|KCNC2|transcript|NM_153748.2|protein_coding|2/5|c.653T>C|p.Leu218Pro|1214/3400|653/1677|218/558|| GT:GQ:DP:AD:ADF:ADR 0/0:.:21:21,0:9,0:12,0 0/1:.:57:50,7:20,4:30,3 +chr12 109999777 rs1889849841 A G . PASS DP=67;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.099397;FREQ=TOMMO:0.9961,0.003878;GENEINFO=ANKRD13A:88455;INT;NSM;SSR=0;U5;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=1;SIFT_pred=T;Polyphen2_HDIV_score=0.0;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.001;Polyphen2_HVAR_pred=B;LRT_score=0.090;LRT_pred=N;MutationTaster_score=0.835;MutationTaster_pred=D;MutationAssessor_score=0.315;MutationAssessor_pred=N;FATHMM_score=-0.11;FATHMM_pred=T;RadialSVM_score=-0.977;RadialSVM_pred=T;LR_score=0.089;LR_pred=T;VEST3_score=0.07;CADD_raw=0.273;CADD_phred=5.475;GERP++_RS=1.08;phyloP46way_placental=0.419;phyloP100way_vertebrate=0.106;SiPhy_29way_logOdds=7.367;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=G|missense_variant|MODERATE|ANKRD13A|ANKRD13A|transcript|NM_033121.1|protein_coding|1/15|c.89A>G|p.Gln30Arg|348/3908|89/1773|30/590||,G|upstream_gene_variant|MODIFIER|GIT2|GIT2|transcript|NM_057169.4|protein_coding||c.-3553T>C|||||3388|,G|upstream_gene_variant|MODIFIER|GIT2|GIT2|transcript|NM_001135213.2|protein_coding||c.-3553T>C|||||3388|,G|upstream_gene_variant|MODIFIER|GIT2|GIT2|transcript|NM_001135214.2|protein_coding||c.-3553T>C|||||3388|,G|upstream_gene_variant|MODIFIER|GIT2|GIT2|transcript|NM_001330153.1|protein_coding||c.-3553T>C|||||3388|,G|upstream_gene_variant|MODIFIER|GIT2|GIT2|transcript|NM_014776.4|protein_coding||c.-3553T>C|||||3388|,G|upstream_gene_variant|MODIFIER|GIT2|GIT2|transcript|NM_057170.4|protein_coding||c.-3553T>C|||||3388|,G|upstream_gene_variant|MODIFIER|GIT2|GIT2|transcript|NM_001330154.1|protein_coding||c.-3553T>C|||||3388|,G|upstream_gene_variant|MODIFIER|GIT2|GIT2|transcript|NM_139201.2|protein_coding||c.-3553T>C|||||3388| GT:GQ:DP:AD:ADF:ADR 0/0:.:14:14,0:12,0:2,0 0/1:.:53:43,9:37,1:6,8 +chr13 36845100 . ATGTG A . MinMMQSdiff DP=122;SOMATIC;SS=2;SSC=14;GPV=1;SPV=0.036896;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=336095;CLNDN=Primary_pulmonary_hypertension_1;CLNDISDB=MONDO:MONDO:0024533,MedGen:C4552070,OMIM:178600;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;ALLELE_END;ANN=A|3_prime_UTR_variant|MODIFIER|SMAD9|SMAD9|transcript|NM_001127217.2|protein_coding|7/7|c.*3572_*3575delCACA|||||3572|,A|3_prime_UTR_variant|MODIFIER|SMAD9|SMAD9|transcript|NM_005905.5|protein_coding|6/6|c.*3572_*3575delCACA|||||3572| GT:GQ:DP:AD:ADF:ADR 0/0:.:33:33,0:16,0:17,0 0/1:.:89:79,10:42,9:37,1 +chr14 53055920 . T TA . MinMMQSdiff DP=180;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.070254;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=685399;CLNDN=Spastic_paraplegia_28,_autosomal_recessive;CLNDISDB=MONDO:MONDO:0012256,MedGen:C1836295,OMIM:609340,Orphanet:ORPHA101008;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Benign;ALLELE_END;ANN=TA|intron_variant|MODIFIER|DDHD1|DDHD1|transcript|NM_001160148.1|protein_coding|9/12|c.1993-9dupT||||||,TA|intron_variant|MODIFIER|DDHD1|DDHD1|transcript|NM_001160147.1|protein_coding|10/12|c.2014-9dupT||||||,TA|intron_variant|MODIFIER|DDHD1|DDHD1|transcript|NM_030637.2|protein_coding|9/11|c.1993-9dupT|||||| GT:GQ:DP:AD:ADF:ADR 0/0:.:49:49,0:29,0:20,0 0/1:.:131:120,8:60,2:60,6 +chr14 60282825 . C T . PASS DP=137;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10575;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.02;SIFT_pred=D;Polyphen2_HDIV_score=0.984;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.564;Polyphen2_HVAR_pred=P;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=2.18;MutationAssessor_pred=M;FATHMM_score=2.25;FATHMM_pred=T;RadialSVM_score=-1.090;RadialSVM_pred=T;LR_score=0.081;LR_pred=T;VEST3_score=0.891;CADD_raw=4.216;CADD_phred=21.9;GERP++_RS=5.75;phyloP46way_placental=2.704;phyloP100way_vertebrate=7.818;SiPhy_29way_logOdds=19.923;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=T|structural_interaction_variant|HIGH|PPM1A|PPM1A|interaction|1A6Q:A_41-A_72:NM_021003.4|protein_coding|2/6|c.122C>T||||||,T|structural_interaction_variant|HIGH|PPM1A|PPM1A|interaction|3FXJ:A_41-A_72:NM_021003.4|protein_coding|2/6|c.122C>T||||||,T|structural_interaction_variant|HIGH|PPM1A|PPM1A|interaction|3FXK:A_41-A_72:NM_021003.4|protein_coding|2/6|c.122C>T||||||,T|structural_interaction_variant|HIGH|PPM1A|PPM1A|interaction|3FXL:A_41-A_72:NM_021003.4|protein_coding|2/6|c.122C>T||||||,T|structural_interaction_variant|HIGH|PPM1A|PPM1A|interaction|3FXM:A_41-A_72:NM_021003.4|protein_coding|2/6|c.122C>T||||||,T|structural_interaction_variant|HIGH|PPM1A|PPM1A|interaction|3FXO:A_41-A_72:NM_021003.4|protein_coding|2/6|c.122C>T||||||,T|structural_interaction_variant|HIGH|PPM1A|PPM1A|interaction|4RA2:A_41-A_72:NM_021003.4|protein_coding|2/6|c.122C>T||||||,T|missense_variant|MODERATE|PPM1A|PPM1A|transcript|NM_177952.2|protein_coding|2/6|c.341C>T|p.Thr114Met|437/8069|341/1368|114/455||,T|missense_variant|MODERATE|PPM1A|PPM1A|transcript|NM_177951.2|protein_coding|3/4|c.122C>T|p.Thr41Met|674/4317|122/975|41/324||,T|missense_variant|MODERATE|PPM1A|PPM1A|transcript|NM_021003.4|protein_coding|2/6|c.122C>T|p.Thr41Met|572/8204|122/1149|41/382|| GT:GQ:DP:AD:ADF:ADR 0/0:.:42:42,0:18,0:24,0 0/1:.:95:89,6:39,4:50,2 +chr14 73064954 . C CT . MinMMQSdiff DP=141;SOMATIC;SS=2;SSC=20;GPV=1;SPV=0.0082366;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=794309;CLNDN=CIC-DUX_Sarcoma;CLNDISDB=MedGen:C3899764;CLNREVSTAT=no_assertion_provided;CLNSIG=not_provided;ALLELE_END;ANN=CT|intron_variant|MODIFIER|RBM25|RBM25|transcript|NM_021239.2|protein_coding|1/18|c.-16+6264dupT||||||INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR 0/0:.:47:41,0:23,0:18,0 0/1:.:94:77,12:40,4:37,8 +chr14 95535217 . A G . PASS DP=25;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.093333;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.03;SIFT_pred=D;Polyphen2_HDIV_score=0.09;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.009;Polyphen2_HVAR_pred=B;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=2.94;MutationAssessor_pred=M;FATHMM_score=1.25;FATHMM_pred=T;RadialSVM_score=-0.923;RadialSVM_pred=T;LR_score=0.126;LR_pred=T;VEST3_score=0.231;CADD_raw=3.581;CADD_phred=18.24;GERP++_RS=3.55;phyloP46way_placental=0.813;phyloP100way_vertebrate=3.504;SiPhy_29way_logOdds=10.604;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=G|missense_variant|MODERATE|GLRX5|GLRX5|transcript|NM_016417.2|protein_coding|1/2|c.128A>G|p.Glu43Gly|232/1171|128/474|43/157||,G|upstream_gene_variant|MODIFIER|SNHG10|SNHG10|transcript|NR_003138.3|pseudogene||n.-345T>C|||||345|,G|upstream_gene_variant|MODIFIER|SCARNA13|SCARNA13|transcript|NR_003002.1|pseudogene||n.-1588T>C|||||1588|,G|upstream_gene_variant|MODIFIER|SNHG10|SNHG10|transcript|NR_001459.2|pseudogene||n.-345T>C|||||345| GT:GQ:DP:AD:ADF:ADR 0/0:.:17:17,0:2,0:15,0 0/1:.:8:6,2:6,2:0,0 +chr14 104939447 . T C . PASS DP=137;SOMATIC;SS=2;SSC=42;GPV=1;SPV=5.4204e-05;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.38;SIFT_pred=T;Polyphen2_HDIV_score=0.0;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.001;Polyphen2_HVAR_pred=B;LRT_score=0.002;LRT_pred=U;MutationTaster_score=1.000;MutationTaster_pred=N;MutationAssessor_score=-0.345;MutationAssessor_pred=N;FATHMM_score=6.06;FATHMM_pred=T;RadialSVM_score=-0.921;RadialSVM_pred=T;LR_score=0.005;LR_pred=T;VEST3_score=0.032;CADD_raw=-0.972;CADD_phred=0.304;GERP++_RS=-4.01;phyloP46way_placental=-0.747;phyloP100way_vertebrate=-1.890;SiPhy_29way_logOdds=7.542;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|AHNAK2|AHNAK2|transcript|NM_138420.2|protein_coding|7/7|c.16004A>G|p.His5335Arg|16124/18317|16004/17388|5335/5795|| GT:GQ:DP:AD:ADF:ADR 0/0:.:30:30,0:18,0:12,0 0/1:.:107:73,34:35,17:38,17 +chr16 72788664 . T TTGC . MinMMQSdiff DP=85;SOMATIC;SS=2;SSC=16;GPV=1;SPV=0.020937;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=ID\x3dCOSM1379701\x3bOCCURENCE\x3d1(large_intestine);SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=TTGC|disruptive_inframe_insertion|MODERATE|ZFHX3|ZFHX3|transcript|NM_006885.3|protein_coding|10/10|c.9609_9611dupGCA|p.Gln3204dup|10284/16062|9611/11112|3204/3703||,TTGC|disruptive_inframe_insertion|MODERATE|ZFHX3|ZFHX3|transcript|NM_001164766.1|protein_coding|9/9|c.6867_6869dupGCA|p.Gln2290dup|6998/12776|6869/8370|2290/2789|| GT:GQ:DP:AD:ADF:ADR 0/0:.:21:19,2:7,2:12,0 0/1:.:64:39,21:19,12:20,9 +chr17 44248849 . G GT . MinMMQSdiff DP=41;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10791;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=344704;CLNDN=Hemolytic_anemia|Distal_Renal_Tubular_Acidosis,_Dominant|Spherocytosis,_Dominant;CLNDISDB=Human_Phenotype_Ontology:HP:0001878,Human_Phenotype_Ontology:HP:0001910,Human_Phenotype_Ontology:HP:0004827,Human_Phenotype_Ontology:HP:0004853,Human_Phenotype_Ontology:HP:0004868,Human_Phenotype_Ontology:HP:0005503,MONDO:MONDO:0003664,MedGen:C0002878|MedGen:CN239155|MedGen:CN239455;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Uncertain_significance;ALLELE_END;ANN=GT|3_prime_UTR_variant|MODIFIER|SLC4A1|SLC4A1|transcript|NM_000342.3|protein_coding|20/20|c.*1608dupA|||||1608| GT:GQ:DP:AD:ADF:ADR 0/0:.:15:10,0:7,0:3,0 0/1:.:26:11,4:3,2:8,2 +chr17 76736877 rs751713049 G T . PASS DP=41;SOMATIC;SS=2;SSC=16;GPV=1;SPV=0.021382;CLNACC=.,.,RCV001293765.1,.;CLNDISDB=.,.,MONDO:MONDO:0020526/MedGen:CN207426,.;CLNDN=.,.,Acute_megakaryoblastic_leukemia_in_down_syndrome,.;CLNORIGIN=.,.,2,.;CLNREVSTAT=.,.,single,.;CLNSIG=.,.,4,.;FREQ=Korea1K:0.9994,0.0005593,.,.|TOMMO:0.9998,.,.,0.0002388|dbGaP_PopFreq:1,0,0,0;GENEINFO=SRSF2:6427|MFSD11:79157|MIR636:693221;NSM;R5;SSR=0;U5;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=ID\x3dCOSM211029,COSM211505,COSM211504\x3bOCCURENCE\x3d80(haematopoietic_and_lymphoid_tissue);SIFT_score=0.02;SIFT_pred=D;Polyphen2_HDIV_score=1.0;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.984;Polyphen2_HVAR_pred=D;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=2.56;MutationAssessor_pred=M;FATHMM_score=-0.94;FATHMM_pred=T;RadialSVM_score=-0.044;RadialSVM_pred=T;LR_score=0.532;LR_pred=D;VEST3_score=0.311;CADD_raw=2.169;CADD_phred=13.21;GERP++_RS=2.76;phyloP46way_placental=0.413;phyloP100way_vertebrate=8.573;SiPhy_29way_logOdds=8.660;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=T|missense_variant|MODERATE|SRSF2|SRSF2|transcript|NM_001195427.1|protein_coding|1/3|c.284C>A|p.Pro95His|535/1968|284/666|95/221||,T|missense_variant|MODERATE|SRSF2|SRSF2|transcript|NM_003016.4|protein_coding|1/2|c.284C>A|p.Pro95His|535/2963|284/666|95/221||,T|5_prime_UTR_variant|MODIFIER|MFSD11|MFSD11|transcript|NM_001242534.1|protein_coding|1/14|c.-286G>T|||||1476|,T|upstream_gene_variant|MODIFIER|MIR636|MIR636|transcript|NR_030366.1|pseudogene||n.-329C>A|||||329|,T|upstream_gene_variant|MODIFIER|MFSD11|MFSD11|transcript|NM_001242532.1|protein_coding||c.-1476G>T|||||624|,T|upstream_gene_variant|MODIFIER|MFSD11|MFSD11|transcript|NM_001242533.1|protein_coding||c.-1476G>T|||||624|,T|upstream_gene_variant|MODIFIER|MFSD11|MFSD11|transcript|NM_001242535.1|protein_coding||c.-1476G>T|||||624|,T|upstream_gene_variant|MODIFIER|MFSD11|MFSD11|transcript|NM_001242536.1|protein_coding||c.-1476G>T|||||624|,T|upstream_gene_variant|MODIFIER|MFSD11|MFSD11|transcript|NM_001242537.1|protein_coding||c.-1476G>T|||||624|,T|upstream_gene_variant|MODIFIER|MFSD11|MFSD11|transcript|NM_024311.3|protein_coding||c.-1476G>T|||||624|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001080510.4|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001206983.2|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001206984.2|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001206985.2|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001206986.2|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001206987.2|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001302703.1|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001302704.1|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NM_001302705.1|protein_coding||c.*3191G>T|||||2996|,T|downstream_gene_variant|MODIFIER|METTL23|METTL23|transcript|NR_038193.2|pseudogene||n.*2996G>T|||||2996|,T|non_coding_transcript_exon_variant|MODIFIER|SRSF2|SRSF2|transcript|NR_036608.1|pseudogene|1/4|n.535C>A|||||| GT:GQ:DP:AD:ADF:ADR 0/0:.:16:16,0:10,0:6,0 0/1:.:25:18,7:14,2:4,5 +chr19 1065393 . G T . PASS DP=119;SOMATIC;SS=2;SSC=64;GPV=1;SPV=3.6034e-07;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.03;SIFT_pred=D;Polyphen2_HDIV_score=0.979;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.511;Polyphen2_HVAR_pred=P;LRT_score=.;LRT_pred=.;MutationTaster_score=1.000;MutationTaster_pred=N;MutationAssessor_score=0;MutationAssessor_pred=N;FATHMM_score=-2.22;FATHMM_pred=D;RadialSVM_score=-0.593;RadialSVM_pred=T;LR_score=0.375;LR_pred=T;VEST3_score=0.486;CADD_raw=2.144;CADD_phred=13.13;GERP++_RS=1.46;phyloP46way_placental=0.760;phyloP100way_vertebrate=0.687;SiPhy_29way_logOdds=5.290;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=T|missense_variant|MODERATE|ABCA7|ABCA7|transcript|NM_019112.3|protein_coding|47/47|c.6409G>T|p.Asp2137Tyr|6640/6818|6409/6441|2137/2146||,T|upstream_gene_variant|MODIFIER|ARHGAP45|ARHGAP45|transcript|NM_001258328.2|protein_coding||c.-633G>T|||||530|,T|upstream_gene_variant|MODIFIER|ARHGAP45|ARHGAP45|transcript|NM_012292.4|protein_coding||c.-2013G>T|||||1773|,T|upstream_gene_variant|MODIFIER|ARHGAP45|ARHGAP45|transcript|NM_001321232.1|protein_coding||c.-2180G>T|||||2105| GT:GQ:DP:AD:ADF:ADR 0/0:.:32:32,0:21,0:11,0 0/1:.:87:49,38:31,30:18,8 +chr19 10467500 . A G . PASS DP=74;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11838;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0.48;SIFT_pred=T;Polyphen2_HDIV_score=0.001;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.004;Polyphen2_HVAR_pred=B;LRT_score=0.000;LRT_pred=N;MutationTaster_score=0.958;MutationTaster_pred=N;MutationAssessor_score=0;MutationAssessor_pred=N;FATHMM_score=0.21;FATHMM_pred=T;RadialSVM_score=-1.029;RadialSVM_pred=T;LR_score=0.109;LR_pred=T;VEST3_score=0.042;CADD_raw=0.477;CADD_phred=6.589;GERP++_RS=-0.855;phyloP46way_placental=0.043;phyloP100way_vertebrate=0.494;SiPhy_29way_logOdds=6.149;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=G|missense_variant|MODERATE|PDE4A|PDE4A|transcript|NM_001111307.1|protein_coding|15/15|c.2540A>G|p.Glu847Gly|2648/4779|2540/2661|847/886||,G|missense_variant|MODERATE|PDE4A|PDE4A|transcript|NM_001243121.1|protein_coding|17/17|c.2474A>G|p.Glu825Gly|2558/4689|2474/2595|825/864||,G|missense_variant|MODERATE|PDE4A|PDE4A|transcript|NM_001111308.1|protein_coding|15/15|c.2462A>G|p.Glu821Gly|2462/4593|2462/2583|821/860||,G|missense_variant|MODERATE|PDE4A|PDE4A|transcript|NM_001111309.1|protein_coding|15/15|c.2357A>G|p.Glu786Gly|2357/4488|2357/2478|786/825||,G|missense_variant|MODERATE|PDE4A|PDE4A|transcript|NM_006202.2|protein_coding|10/10|c.1823A>G|p.Glu608Gly|2130/4261|1823/1944|608/647|| GT:GQ:DP:AD:ADF:ADR 0/0:.:25:25,0:6,0:19,0 0/1:.:49:44,5:18,4:26,1 +chr19 12721349 rs1966929781 A G . PASS DP=48;SOMATIC;SS=2;SSC=17;GPV=1;SPV=0.018465;FREQ=TOMMO:0.9993,0.0006567;GENEINFO=TNPO2:30000;INT;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=0.992;MutationTaster_pred=N;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=-1.032;RadialSVM_pred=T;LR_score=0.082;LR_pred=T;VEST3_score=.;CADD_raw=1.556;CADD_phred=11.16;GERP++_RS=2.16;phyloP46way_placental=1.245;phyloP100way_vertebrate=-0.288;SiPhy_29way_logOdds=6.333;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=G|intron_variant|MODIFIER|TNPO2|TNPO2|transcript|NM_001136196.1|protein_coding|1/24|c.-13-359T>C||||||,G|intron_variant|MODIFIER|TNPO2|TNPO2|transcript|NM_013433.4|protein_coding|1/24|c.-13-359T>C||||||,G|intron_variant|MODIFIER|TNPO2|TNPO2|transcript|NM_001136195.1|protein_coding|2/25|c.-13-359T>C|||||| GT:GQ:DP:AD:ADF:ADR 0/0:.:13:13,0:8,0:5,0 0/1:.:35:24,11:15,8:9,3 +chr19 45795880 . T TCTCCTCGCCCTCCTCCTC . MinMMQSdiff DP=102;SOMATIC;SS=2;SSC=19;GPV=1;SPV=0.010588;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=ID\x3dCOSM253920\x3bOCCURENCE\x3d1(urinary_tract);SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=TCTCCTCGCCCTCCTCCTC|conservative_inframe_insertion|MODERATE|RSPH6A|RSPH6A|transcript|NM_030785.3|protein_coding|6/6|c.2125_2142dupGAGGAGGAGGGCGAGGAG|p.Glu714_Thr715insGluGluGluGlyGluGlu|2313/2484|2142/2154|714/717||,TCTCCTCGCCCTCCTCCTC|upstream_gene_variant|MODIFIER|DMWD|DMWD|transcript|NM_004943.1|protein_coding||c.-3142_-3125dupGAGGAGGAGGGCGAGGAG|||||3079| GT:GQ:DP:AD:ADF:ADR 0/0:.:25:24,0:12,0:12,0 0/1:.:77:60,15:36,8:24,7 +chr20 6075049 . G GT . PASS DP=149;SOMATIC;SS=2;SSC=14;GPV=1;SPV=0.037662;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=351325;CLNDN=Kindler_syndrome;CLNDISDB=MONDO:MONDO:0008260,MedGen:C0406557,OMIM:173650,Orphanet:ORPHA2908,SNOMED_CT:238835001,SNOMED_CT:238836000;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Uncertain_significance;ALLELE_END;ANN=GT|3_prime_UTR_variant|MODIFIER|FERMT1|FERMT1|transcript|NM_017671.4|protein_coding|15/15|c.*2123dupA|||||2123| GT:GQ:DP:AD:ADF:ADR 0/0:.:47:45,1:22,0:23,1 0/1:.:102:84,12:37,5:47,7 +chr20 32808191 . CT C . MinMMQSdiff DP=137;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10114;INDEL;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;CLNALLELEID=345075;CLNDN=Immunodeficiency-centromeric_instability-facial_anomalies_syndrome_1;CLNDISDB=MONDO:MONDO:0009454,MedGen:C4551557,OMIM:242860;CLNREVSTAT=criteria_provided,_single_submitter;CLNSIG=Uncertain_significance;ALLELE_END;ANN=C|3_prime_UTR_variant|MODIFIER|DNMT3B|DNMT3B|transcript|NM_006892.3|protein_coding|23/23|c.*299delT|||||299|INFO_REALIGN_3_PRIME,C|3_prime_UTR_variant|MODIFIER|DNMT3B|DNMT3B|transcript|NM_001207055.1|protein_coding|19/19|c.*299delT|||||299|INFO_REALIGN_3_PRIME,C|3_prime_UTR_variant|MODIFIER|DNMT3B|DNMT3B|transcript|NM_001207056.1|protein_coding|18/18|c.*299delT|||||299|INFO_REALIGN_3_PRIME,C|3_prime_UTR_variant|MODIFIER|DNMT3B|DNMT3B|transcript|NM_175848.1|protein_coding|22/22|c.*299delT|||||299|INFO_REALIGN_3_PRIME,C|3_prime_UTR_variant|MODIFIER|DNMT3B|DNMT3B|transcript|NM_175849.1|protein_coding|20/20|c.*299delT|||||299|INFO_REALIGN_3_PRIME,C|3_prime_UTR_variant|MODIFIER|DNMT3B|DNMT3B|transcript|NM_175850.2|protein_coding|22/22|c.*299delT|||||299|INFO_REALIGN_3_PRIME GT:GQ:DP:AD:ADF:ADR 0/0:.:37:36,0:21,0:15,0 0/1:.:100:89,7:46,5:43,2 +chr20 38836101 . G C . PASS DP=82;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.089735;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=1;SIFT_pred=T;Polyphen2_HDIV_score=0.018;Polyphen2_HDIV_pred=B;Polyphen2_HVAR_score=0.02;Polyphen2_HVAR_pred=B;LRT_score=0.175;LRT_pred=N;MutationTaster_score=1.000;MutationTaster_pred=N;MutationAssessor_score=0.105;MutationAssessor_pred=N;FATHMM_score=-0.21;FATHMM_pred=T;RadialSVM_score=-0.989;RadialSVM_pred=T;LR_score=0.100;LR_pred=T;VEST3_score=0.167;CADD_raw=-1.674;CADD_phred=0.012;GERP++_RS=3.46;phyloP46way_placental=1.288;phyloP100way_vertebrate=1.830;SiPhy_29way_logOdds=4.802;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=C|missense_variant|MODERATE|PPP1R16B|PPP1R16B|transcript|NM_015568.3|protein_coding|2/11|c.176G>C|p.Gly59Ala|377/6263|176/1704|59/567||,C|missense_variant|MODERATE|PPP1R16B|PPP1R16B|transcript|NM_001172735.2|protein_coding|2/10|c.176G>C|p.Gly59Ala|377/6137|176/1578|59/525|| GT:GQ:DP:AD:ADF:ADR 0/0:.:23:23,0:14,0:9,0 0/1:.:59:52,7:41,1:11,6 +chr20 63307547 rs759710143 A G . PASS DP=90;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.074052;FREQ=ExAC:1,8.47e-06|GnomAD_exomes:1,4.036e-06|TOPMED:1,3.778e-06|dbGaP_PopFreq:1,0;GENEINFO=COL20A1:57642;NSM;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=0;SIFT_pred=D;Polyphen2_HDIV_score=1.0;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.999;Polyphen2_HVAR_pred=D;LRT_score=0.000;LRT_pred=U;MutationTaster_score=0.999;MutationTaster_pred=D;MutationAssessor_score=4.565;MutationAssessor_pred=H;FATHMM_score=-4.64;FATHMM_pred=D;RadialSVM_score=1.047;RadialSVM_pred=D;LR_score=0.974;LR_pred=D;VEST3_score=0.769;CADD_raw=4.119;CADD_phred=21.2;GERP++_RS=3.92;phyloP46way_placental=1.418;phyloP100way_vertebrate=6.103;SiPhy_29way_logOdds=11.020;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=G|missense_variant|MODERATE|COL20A1|COL20A1|transcript|NM_020882.2|protein_coding|6/36|c.554A>G|p.Asp185Gly|654/4172|554/3855|185/1284|| GT:GQ:DP:AD:ADF:ADR 0/0:.:27:27,0:11,0:16,0 0/1:.:63:56,7:26,6:30,1 +chr21 32361892 rs371227097 C T . PASS DP=118;SOMATIC;SS=2;SSC=45;GPV=1;SPV=3.1599e-05;FREQ=1000Genomes:0.9998,0.0001997|ALSPAC:1,0|ExAC:1,4.72e-05|GnomAD:0.9998,0.0001711|GnomAD_exomes:0.9998,0.0002368|GoESP:0.9998,0.000219|MGP:0.9981,0.001873|TOPMED:0.9998,0.0002116|TWINSUK:0.9992,0.0008091|dbGaP_PopFreq:0.9998,0.0002345;GENEINFO=URB1:9875;NSM;SSR=0;VC=SNV;ANNOVAR_DATE=2020-06-08;cosmic70=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=1.0;Polyphen2_HDIV_pred=D;Polyphen2_HVAR_score=0.926;Polyphen2_HVAR_pred=D;LRT_score=0.000;LRT_pred=D;MutationTaster_score=1.000;MutationTaster_pred=D;MutationAssessor_score=2.045;MutationAssessor_pred=M;FATHMM_score=1.49;FATHMM_pred=T;RadialSVM_score=-0.911;RadialSVM_pred=T;LR_score=0.169;LR_pred=T;VEST3_score=0.087;CADD_raw=3.753;CADD_phred=19.05;GERP++_RS=5.26;phyloP46way_placental=2.608;phyloP100way_vertebrate=1.875;SiPhy_29way_logOdds=15.945;CLNALLELEID=.;CLNDN=.;CLNDISDB=.;CLNREVSTAT=.;CLNSIG=.;ALLELE_END;ANN=T|missense_variant&splice_region_variant|MODERATE|URB1|URB1|transcript|NM_014825.2|protein_coding|12/39|c.1639G>A|p.Asp547Asn|1732/10808|1639/6816|547/2271|| GT:GQ:DP:AD:ADF:ADR 0/0:.:31:31,0:14,0:17,0 0/1:.:87:58,29:31,16:27,13
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcf_2.vcf Mon Nov 28 21:59:34 2022 +0000 @@ -0,0 +1,247 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=PASS,Description="All filters passed"> +##reference=/home/galaxy/galaxy/tool-data/hg38-bgi-light/sam_indexes/hg38-bgi-light/hg38-bgi-light.fa +##source=varscan.py +##contig=<ID=chr1,length=248956422> +##contig=<ID=chr10,length=133797422> +##contig=<ID=chr11,length=135086622> +##contig=<ID=chr12,length=133275309> +##contig=<ID=chr13,length=114364328> +##contig=<ID=chr14,length=107043718> +##contig=<ID=chr15,length=101991189> +##contig=<ID=chr16,length=90338345> +##contig=<ID=chr17,length=83257441> +##contig=<ID=chr18,length=80373285> +##contig=<ID=chr19,length=58617616> +##contig=<ID=chr2,length=242193529> +##contig=<ID=chr20,length=64444167> +##contig=<ID=chr21,length=46709983> +##contig=<ID=chr22,length=50818468> +##contig=<ID=chr3,length=198295559> +##contig=<ID=chr4,length=190214555> +##contig=<ID=chr5,length=181538259> +##contig=<ID=chr6,length=170805979> +##contig=<ID=chr7,length=159345973> +##contig=<ID=chr8,length=145138636> +##contig=<ID=chr9,length=138394717> +##contig=<ID=chrM,length=16569> +##contig=<ID=chrX,length=156040895> +##contig=<ID=chrY,length=57227415> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases"> +##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation"> +##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)"> +##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value"> +##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls"> +##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls"> +##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand"> +##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position"> +##FILTER=<ID=VarCount,Description="Fewer than 4 variant-supporting reads"> +##FILTER=<ID=VarFreq,Description="Variant allele frequency below 0.05"> +##FILTER=<ID=VarAvgRL,Description="Average clipped length of variant-supporting reads < 90"> +##FILTER=<ID=VarReadPos,Description="Relative average read position < 0.1"> +##FILTER=<ID=VarDist3,Description="Average distance to effective 3' end < 0.1"> +##FILTER=<ID=VarMMQS,Description="Average mismatch quality sum for variant reads > 100"> +##FILTER=<ID=VarMapQual,Description="Average mapping quality of variant reads < 15"> +##FILTER=<ID=VarBaseQual,Description="Average base quality of variant reads < 15"> +##FILTER=<ID=Strand,Description="Strand representation of variant reads < 0.01"> +##FILTER=<ID=RefAvgRL,Description="Average clipped length of ref-supporting reads < 90"> +##FILTER=<ID=RefReadPos,Description="Relative average read position < 0.1"> +##FILTER=<ID=RefDist3,Description="Average distance to effective 3' end < 0.1"> +##FILTER=<ID=RefMapQual,Description="Average mapping quality of reference reads < 15"> +##FILTER=<ID=RefBaseQual,Description="Average base quality of ref-supporting reads < 15"> +##FILTER=<ID=RefMMQS,Description="Average mismatch quality sum for ref-supporting reads > 100"> +##FILTER=<ID=MMQSdiff,Description="Mismatch quality sum difference (var - ref) > 50"> +##FILTER=<ID=MinMMQSdiff,Description="Mismatch quality sum difference (var - ref) < 50"> +##FILTER=<ID=MapQualDiff,Description="Mapping quality difference (ref - var) > 50"> +##FILTER=<ID=MaxBAQdiff,Description="Average base quality difference (ref - var) > 50"> +##FILTER=<ID=ReadLenDiff,Description="Average supporting read length difference (ref - var) > 0.25"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype code"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth"> +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Read depth for each allele"> +##FORMAT=<ID=ADF,Number=R,Type=Integer,Description="Read depth for each allele on the forward strand"> +##FORMAT=<ID=ADR,Number=R,Type=Integer,Description="Read depth for each allele on the reverse strand"> +##bcftools_filterVersion=1.10.2+htslib-1.10.2 +##bcftools_filterCommand=filter --include 'INFO/SPV < 0.12 | INFO/GPV < 0.12' --output-type v --threads 1 input.vcf.gz; Date=Thu Apr 21 00:52:51 2022 +##bcftools_concatVersion=1.10.2+htslib-1.10.2 +##bcftools_concatCommand=concat --allow-overlaps --min-PQ 30 --output-type v --threads 1 input0.vcf.gz input1.vcf.gz input2.vcf.gz input3.vcf.gz input4.vcf.gz input5.vcf.gz input6.vcf.gz input7.vcf.gz input8.vcf.gz input9.vcf.gz input10.vcf.gz input11.vcf.gz input12.vcf.gz input13.vcf.gz input14.vcf.gz input15.vcf.gz input16.vcf.gz input17.vcf.gz input18.vcf.gz input19.vcf.gz input20.vcf.gz input21.vcf.gz input22.vcf.gz input23.vcf.gz input24.vcf.gz; Date=Thu Apr 21 00:53:11 2022 +##bcftools_filterCommand=filter --regions-file regions_file.bed --output-type v --threads 1 input.vcf.gz; Date=Wed Sep 7 23:57:08 2022 +##bcftools_filterCommand=filter --include 'FILTER ~ "PASS" | FILTER ~ "MinMMQSdiff" | FILTER ~ "RefReadPos"' --output-type v --threads 1 input.vcf.gz; Date=Thu Sep 8 00:00:22 2022 +##bcftools_viewVersion=1.10.2+htslib-1.10.2 +##bcftools_viewCommand=view --output-type v; Date=Thu Sep 8 00:00:33 2022 +##bcftools_filterCommand=filter --include 'INFO/SS ~ "2"' --output-type v --threads 1 input.vcf.gz; Date=Thu Sep 8 00:00:44 2022 +##SnpSiftVersion="SnpSift 4.3t (build 2017-11-24 10:18), by Pablo Cingolani" +##SnpSiftCmd="SnpSift Annotate -info GENEINFO,PSEUDOGENEINFO,SAO,SSR,VC,NSF,NSM,NSN,SYN,U3,U5,ASS,DSS,INT,R3,R5,FREQ,COMMON,CLNVI,CLNORIGIN,CLNSIG,CLNDISDB,CLNDN,CLNREVSTAT,CLNACC dbSnp.vcf /home/galaxy/galaxy/database/datasets/001/336/dataset_1336409.dat" +##INFO=<ID=NSF,Number=0,Type=Flag,Description="Has non-synonymous frameshift A coding region variation where one allele in the set changes all downstream amino acids. FxnClass = 44"> +##INFO=<ID=R3,Number=0,Type=Flag,Description="In 3' gene region FxnCode = 13"> +##INFO=<ID=R5,Number=0,Type=Flag,Description="In 5' gene region FxnCode = 15"> +##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Variant Clinical Significance, 0 - Uncertain significance, 1 - not provided, 2 - Benign, 3 - Likely benign, 4 - Likely pathogenic, 5 - Pathogenic, 6 - drug response, 8 - confers sensitivity, 9 - risk-factor, 10 - association, 11 - protective, 12 - conflict, 13 - affects, 255 - other"> +##INFO=<ID=NSN,Number=0,Type=Flag,Description="Has non-synonymous nonsense A coding region variation where one allele in the set changes to STOP codon (TER). FxnClass = 41"> +##INFO=<ID=NSM,Number=0,Type=Flag,Description="Has non-synonymous missense A coding region variation where one allele in the set changes protein peptide. FxnClass = 42"> +##INFO=<ID=CLNORIGIN,Number=.,Type=String,Description="Allele Origin. One or more of the following values may be summed: 0 - unknown; 1 - germline; 2 - somatic; 4 - inherited; 8 - paternal; 16 - maternal; 32 - de-novo; 64 - biparental; 128 - uniparental; 256 - not-tested; 512 - tested-inconclusive; 1073741824 - other"> +##INFO=<ID=CLNREVSTAT,Number=.,Type=String,Description="ClinVar Review Status: no_assertion - No asserition provided by submitter, no_criteria - No assertion criteria provided by submitter, single - Classified by single submitter, mult - Classified by multiple submitters, conf - Criteria provided conflicting interpretations, exp - Reviewed by expert panel, guideline - Practice guideline"> +##INFO=<ID=COMMON,Number=0,Type=Flag,Description="RS is a common SNP. A common SNP is one that has at least one 1000Genomes population with a minor allele of frequency >= 1% and for which 2 or more founders contribute to that minor allele frequency."> +##INFO=<ID=FREQ,Number=.,Type=String,Description="An ordered list of allele frequencies as reported by various genomic studies starting with the reference allele followed by alternate alleles as ordered in the ALT column. When not already in the dbSNP allele set alleles from the studies are added to the ALT column. The minor allele which was previuosly reported in VCF as the GMAF is the second largest value in the list. This is the GMAF reported on the RefSNP and EntrezSNP pages and VariationReporter"> +##INFO=<ID=ASS,Number=0,Type=Flag,Description="In acceptor splice site FxnCode = 73"> +##INFO=<ID=U3,Number=0,Type=Flag,Description="In 3' UTR Location is in an untranslated region (UTR). FxnCode = 53"> +##INFO=<ID=U5,Number=0,Type=Flag,Description="In 5' UTR Location is in an untranslated region (UTR). FxnCode = 55"> +##INFO=<ID=CLNACC,Number=.,Type=String,Description="For each allele (comma delimited), this is a pipe-delimited list of the Clinvar RCV phenotype accession.version strings associated with that allele."> +##INFO=<ID=CLNDN,Number=.,Type=String,Description="Preferred ClinVar disease name"> +##INFO=<ID=DSS,Number=0,Type=Flag,Description="In donor splice-site FxnCode = 75"> +##INFO=<ID=SYN,Number=0,Type=Flag,Description="Has synonymous A coding region variation where one allele in the set does not change the encoded amino acid. FxnCode = 3"> +##INFO=<ID=CLNVI,Number=.,Type=String,Description="Variant Identifiers provided and maintained by organizations outside of NCBI, such as OMIM. Source and id separated by colon (:). Each identifier is separated by a vertical bar (|)"> +##INFO=<ID=VC,Number=1,Type=String,Description="Variation Class"> +##INFO=<ID=SAO,Number=1,Type=Integer,Description="Variant Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both"> +##INFO=<ID=PSEUDOGENEINFO,Number=1,Type=String,Description="Pairs each of pseudogene symbol:gene id. The pseudogene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|)"> +##INFO=<ID=CLNDISDB,Number=.,Type=String,Description="Variant disease database name and ID, separated by colon (:)"> +##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|). Does not include pseudogenes."> +##INFO=<ID=INT,Number=0,Type=Flag,Description="In Intron FxnCode = 6"> +##INFO=<ID=SSR,Number=1,Type=Integer,Description="Variant Suspect Reason Codes (may be more than one value added together) 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other"> +##bcftools_concatCommand=concat --allow-overlaps --min-PQ 30 --output-type v --threads 1 input0.vcf.gz input1.vcf.gz input2.vcf.gz input3.vcf.gz input4.vcf.gz input5.vcf.gz input6.vcf.gz input7.vcf.gz input8.vcf.gz input9.vcf.gz input10.vcf.gz input11.vcf.gz input12.vcf.gz input13.vcf.gz input14.vcf.gz input15.vcf.gz input16.vcf.gz input17.vcf.gz input18.vcf.gz input19.vcf.gz input20.vcf.gz input21.vcf.gz input22.vcf.gz input23.vcf.gz input24.vcf.gz; Date=Thu Sep 8 00:04:57 2022 +##bcftools_filterCommand=filter --include 'INFO/COMMON = 0' --output-type v --threads 1 input.vcf.gz; Date=Thu Sep 8 00:05:02 2022 +##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani" +##SnpEffCmd="SnpEff -i vcf -o vcf -stats /home/galaxy/galaxy/database/datasets/001/336/dataset_1336462.dat hg38 /home/galaxy/galaxy/database/datasets/001/336/dataset_1336460.dat " +##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'"> +##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'"> +##INFO=<ID=ANNOVAR_DATE,Number=1,Type=String,Description="Flag the start of ANNOVAR annotation for one alternative allele"> +##INFO=<ID=cosmic70,Number=.,Type=String,Description="cosmic70 annotation provided by ANNOVAR"> +##INFO=<ID=SIFT_score,Number=.,Type=String,Description="SIFT_score annotation provided by ANNOVAR"> +##INFO=<ID=SIFT_pred,Number=.,Type=String,Description="SIFT_pred annotation provided by ANNOVAR"> +##INFO=<ID=Polyphen2_HDIV_score,Number=.,Type=String,Description="Polyphen2_HDIV_score annotation provided by ANNOVAR"> +##INFO=<ID=Polyphen2_HDIV_pred,Number=.,Type=String,Description="Polyphen2_HDIV_pred annotation provided by ANNOVAR"> +##INFO=<ID=Polyphen2_HVAR_score,Number=.,Type=String,Description="Polyphen2_HVAR_score annotation provided by ANNOVAR"> +##INFO=<ID=Polyphen2_HVAR_pred,Number=.,Type=String,Description="Polyphen2_HVAR_pred annotation provided by ANNOVAR"> +##INFO=<ID=LRT_score,Number=.,Type=String,Description="LRT_score annotation provided by ANNOVAR"> +##INFO=<ID=LRT_pred,Number=.,Type=String,Description="LRT_pred annotation provided by ANNOVAR"> +##INFO=<ID=MutationTaster_score,Number=.,Type=String,Description="MutationTaster_score annotation provided by ANNOVAR"> +##INFO=<ID=MutationTaster_pred,Number=.,Type=String,Description="MutationTaster_pred annotation provided by ANNOVAR"> +##INFO=<ID=MutationAssessor_score,Number=.,Type=String,Description="MutationAssessor_score annotation provided by ANNOVAR"> +##INFO=<ID=MutationAssessor_pred,Number=.,Type=String,Description="MutationAssessor_pred annotation provided by ANNOVAR"> +##INFO=<ID=FATHMM_score,Number=.,Type=String,Description="FATHMM_score annotation provided by ANNOVAR"> +##INFO=<ID=FATHMM_pred,Number=.,Type=String,Description="FATHMM_pred annotation provided by ANNOVAR"> +##INFO=<ID=RadialSVM_score,Number=.,Type=String,Description="RadialSVM_score annotation provided by ANNOVAR"> +##INFO=<ID=RadialSVM_pred,Number=.,Type=String,Description="RadialSVM_pred annotation provided by ANNOVAR"> +##INFO=<ID=LR_score,Number=.,Type=String,Description="LR_score annotation provided by ANNOVAR"> +##INFO=<ID=LR_pred,Number=.,Type=String,Description="LR_pred annotation provided by ANNOVAR"> +##INFO=<ID=VEST3_score,Number=.,Type=String,Description="VEST3_score annotation provided by ANNOVAR"> +##INFO=<ID=CADD_raw,Number=.,Type=String,Description="CADD_raw annotation provided by ANNOVAR"> +##INFO=<ID=CADD_phred,Number=.,Type=String,Description="CADD_phred annotation provided by ANNOVAR"> +##INFO=<ID=GERP++_RS,Number=.,Type=String,Description="GERP++_RS annotation provided by ANNOVAR"> +##INFO=<ID=phyloP46way_placental,Number=.,Type=String,Description="phyloP46way_placental annotation provided by ANNOVAR"> +##INFO=<ID=phyloP100way_vertebrate,Number=.,Type=String,Description="phyloP100way_vertebrate annotation provided by ANNOVAR"> +##INFO=<ID=SiPhy_29way_logOdds,Number=.,Type=String,Description="SiPhy_29way_logOdds annotation provided by ANNOVAR"> +##INFO=<ID=CLNALLELEID,Number=.,Type=String,Description="CLNALLELEID annotation provided by ANNOVAR"> +##INFO=<ID=ALLELE_END,Number=0,Type=Flag,Description="Flag the end of ANNOVAR annotation for one alternative allele"> +##bcftools_filterCommand=filter --include 'INFO/LOF != "." | INFO/CLNSIG != "." | INFO/cosmic70 != "." | INFO/Polyphen2_HDIV_pred != "." | INFO/LRT_pred != "." | INFO/MutationTaster_pred != "." | INFO/MutationAssessor_pred != "." | INFO/FATHMM_pred != "."' --output-type v --threads 1 input.vcf.gz; Date=Thu Sep 8 00:06:53 2022 +##SnpEffCmd="SnpEff -i vcf -o vcf -stats /home/galaxy/galaxy/database/datasets/001/336/dataset_1336466.dat hg38 /home/galaxy/galaxy/database/datasets/001/336/dataset_1336464.dat " +##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' "> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 01004_normal 01004_tumor +chr1 11650684 . A C . PASS DP=47;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11479 GT:GQ:DP:AD:ADF:ADR 0/0:.:19:19,0:12,0:7,0 0/1:.:28:24,4:14,1:10,3 +chr1 16058496 rs1323290807 A G . PASS DP=142;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.099679;GENEINFO=FAM131C:348487;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:39:39,0:19,0:20,0 0/1:.:103:96,7:48,6:48,1 +chr1 27012594 rs1310186400 A C . PASS DP=54;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.090013;FREQ=GnomAD_exomes:1,.,7.598e-06|TOMMO:0.9985,0.001492,.;GENEINFO=TENT5B:115572;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:17:17,0:7,0:10,0 0/1:.:37:31,6:18,1:13,5 +chr1 44650749 rs201065980 G A . PASS DP=103;SOMATIC;SS=2;SSC=66;GPV=1;SPV=2.1118e-07;FREQ=1000Genomes:0.9998,0.0001997|ExAC:0.9999,0.0001247|GnomAD:1,2.139e-05|GnomAD_exomes:0.9999,0.0001238|Korea1K:0.9995,0.0005459|TOMMO:0.9994,0.0005967|TOPMED:1,2.645e-05|dbGaP_PopFreq:0.9999,8.681e-05;GENEINFO=RNF220:55182;NSM;R3;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:26:26,0:15,0:11,0 0/1:.:77:37,40:16,16:21,24 +chr1 48736294 . C CT . MinMMQSdiff DP=149;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10454;INDEL;LOF=(BEND5|BEND5|2|1.00) GT:GQ:DP:AD:ADF:ADR 0/0:.:46:45,0:25,0:20,0 0/1:.:103:95,6:44,4:51,2 +chr1 167553617 . T C . PASS DP=35;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.1143 GT:GQ:DP:AD:ADF:ADR 0/0:.:14:14,0:10,0:4,0 0/1:.:21:17,4:6,1:11,3 +chr1 181798751 . A G . PASS DP=63;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10662 GT:GQ:DP:AD:ADF:ADR 0/0:.:22:22,0:12,0:10,0 0/1:.:41:36,5:17,4:19,1 +chr1 200998483 rs777255666 A C . PASS DP=111;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11947;FREQ=ExAC:1,8.281e-06|Korea1K:0.9973,0.002729;GENEINFO=KIF21B:23046;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:28:28,0:18,0:10,0 0/1:.:83:75,7:44,1:31,6 +chr1 235138181 . CA C . MinMMQSdiff DP=128;SOMATIC;SS=2;SSC=15;GPV=1;SPV=0.028543;INDEL GT:GQ:DP:AD:ADF:ADR 0/0:.:50:42,3:21,3:21,0 0/1:.:78:60,16:31,8:29,8 +chr1 235775088 . TA T . MinMMQSdiff DP=181;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.086694;INDEL GT:GQ:DP:AD:ADF:ADR 0/0:.:53:51,0:25,0:26,0 0/1:.:128:118,7:63,3:55,4 +chr2 3702436 . T C . PASS DP=100;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.069291 GT:GQ:DP:AD:ADF:ADR 0/0:.:35:35,0:27,0:8,0 0/1:.:65:59,6:41,1:18,5 +chr2 5693166 . A G . PASS DP=59;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.047667 GT:GQ:DP:AD:ADF:ADR 0/0:.:13:13,0:5,0:8,0 0/1:.:46:35,11:15,9:20,2 +chr2 30232202 rs1677600959 A G . PASS DP=25;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11647;FREQ=GnomAD:1,8.673e-06|dbGaP_PopFreq:1,0;GENEINFO=LBH:81606;INT;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:8:8,0:6,0:2,0 0/1:.:17:12,5:10,4:2,1 +chr2 152148302 . TA T . PASS DP=118;SOMATIC;SS=2;SSC=12;GPV=1;SPV=0.057995;INDEL GT:GQ:DP:AD:ADF:ADR 0/0:.:30:29,0:12,0:17,0 0/1:.:88:73,9:45,5:28,4 +chr2 229271024 rs1690724066 T C . PASS DP=58;SOMATIC;SS=2;SSC=15;GPV=1;SPV=0.027364;FREQ=TOMMO:0.9987,0.001313;GENEINFO=PID1:55022;NSM;R5;SSR=0;U5;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:25:25,0:11,0:14,0 0/1:.:33:27,6:9,2:18,4 +chr3 24118973 . G GT . MinMMQSdiff DP=53;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.044075;INDEL GT:GQ:DP:AD:ADF:ADR 0/0:.:23:17,1:12,0:5,1 0/1:.:30:15,7:12,4:3,3 +chr3 32953733 rs1575380659 T G . PASS DP=166;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.096467;FREQ=Korea1K:0.988,0.01201|dbGaP_PopFreq:1,4.677e-05;GENEINFO=CCR4:1233;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:46:46,0:22,0:24,0 0/1:.:120:112,7:46,4:66,3 +chr3 38485666 . CTTT C . PASS DP=33;SOMATIC;SS=2;SSC=16;GPV=1;SPV=0.023839;INDEL GT:GQ:DP:AD:ADF:ADR 0/0:.:12:6,0:4,0:2,0 0/1:.:21:6,8:4,3:2,5 +chr3 108505838 . CA C . MinMMQSdiff DP=164;SOMATIC;SS=2;SSC=14;GPV=1;SPV=0.037929;INDEL GT:GQ:DP:AD:ADF:ADR 0/0:.:44:36,0:20,0:16,0 0/1:.:120:98,11:61,6:37,5 +chr3 129315500 rs2071293837 T G . PASS DP=29;SOMATIC;SS=2;SSC=23;GPV=1;SPV=0.0041229;FREQ=TOMMO:0.9963,0.003703;GENEINFO=H1-10:8971|H1-10-AS1:339942;NSM;R5;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:14:14,0:8,0:6,0 0/1:.:15:8,7:5,4:3,3 +chr4 122187879 . A AT . MinMMQSdiff DP=164;SOMATIC;SS=2;SSC=17;GPV=1;SPV=0.019764;INDEL;LOF=(KIAA1109|KIAA1109|1|1.00) GT:GQ:DP:AD:ADF:ADR 0/0:.:39:37,0:22,0:15,0 0/1:.:125:107,14:56,5:51,9 +chr5 137677661 . CA C . MinMMQSdiff DP=115;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10535;INDEL GT:GQ:DP:AD:ADF:ADR 0/0:.:29:21,0:12,0:9,0 0/1:.:86:69,9:37,6:32,3 +chr5 160092476 rs1755181710 T C . PASS DP=139;SOMATIC;SS=2;SSC=18;GPV=1;SPV=0.013;FREQ=TOMMO:0.9967,0.003282;GENEINFO=PWWP2A:114825;INT;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:47:47,0:25,0:22,0 0/1:.:92:81,10:22,9:59,1 +chr5 177257228 . C CT . MinMMQSdiff DP=58;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.1043;INDEL GT:GQ:DP:AD:ADF:ADR 0/0:.:18:13,0:5,0:8,0 0/1:.:40:25,6:15,3:10,3 +chr6 35823448 . T TAC . PASS DP=62;SOMATIC;SS=2;SSC=15;GPV=1;SPV=0.026386;INDEL GT:GQ:DP:AD:ADF:ADR 0/0:.:18:16,1:12,0:4,1 0/1:.:44:26,13:16,11:10,2 +chr6 36200360 . A G . PASS DP=113;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.065653 GT:GQ:DP:AD:ADF:ADR 0/0:.:31:31,0:16,0:15,0 0/1:.:82:72,8:37,4:35,4 +chr6 39934360 . T C . PASS DP=48;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11077 GT:GQ:DP:AD:ADF:ADR 0/0:.:16:16,0:9,0:7,0 0/1:.:32:26,5:14,1:12,4 +chr6 87701546 . T G . PASS DP=34;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.044477 GT:GQ:DP:AD:ADF:ADR 0/0:.:17:17,0:7,0:10,0 0/1:.:17:12,4:3,2:9,2 +chr6 113859846 . A G . PASS DP=21;SOMATIC;SS=2;SSC=12;GPV=1;SPV=0.055138 GT:GQ:DP:AD:ADF:ADR 0/0:.:10:10,0:2,0:8,0 0/1:.:11:7,4:7,4:0,0 +chr6 138107153 . T C . PASS DP=52;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.077483 GT:GQ:DP:AD:ADF:ADR 0/0:.:20:20,0:8,0:12,0 0/1:.:32:27,5:4,1:23,4 +chr6 152278138 rs2093774796 C T . PASS DP=103;SOMATIC;SS=2;SSC=57;GPV=1;SPV=1.9582e-06;FREQ=GnomAD:1,7.127e-06|TOPMED:1,3.778e-06|dbGaP_PopFreq:1,0;GENEINFO=SYNE1:23345;NSM;R5;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:21:21,0:15,0:6,0 0/1:.:82:39,43:18,25:21,18 +chr7 44082410 rs2096202919 A C . PASS DP=62;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.043;FREQ=GnomAD:1,7.144e-06|TOPMED:1,1.511e-05|dbGaP_PopFreq:1,0;GENEINFO=POLM:27434;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:28:28,0:10,0:18,0 0/1:.:34:29,5:13,1:16,4 +chr7 100577295 . A C . PASS DP=66;SOMATIC;SS=2;SSC=17;GPV=1;SPV=0.01619 GT:GQ:DP:AD:ADF:ADR 0/0:.:22:22,0:12,0:10,0 0/1:.:44:33,9:23,2:10,7 +chr7 129225249 . A G . PASS DP=19;SOMATIC;SS=2;SSC=12;GPV=1;SPV=0.05418 GT:GQ:DP:AD:ADF:ADR 0/0:.:9:9,0:3,0:6,0 0/1:.:10:6,4:6,4:0,0 +chr7 137015017 . A C . PASS DP=154;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.092245 GT:GQ:DP:AD:ADF:ADR 0/0:.:49:49,0:25,0:24,0 0/1:.:105:97,6:56,1:41,5 +chr8 64616285 . G GA . PASS DP=152;SOMATIC;SS=2;SSC=16;GPV=1;SPV=0.022125;INDEL GT:GQ:DP:AD:ADF:ADR 0/0:.:53:49,0:23,0:26,0 0/1:.:99:88,9:52,7:36,2 +chr8 85662359 rs1814217731 A G . PASS DP=188;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11249;FREQ=dbGaP_PopFreq:1,0;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:56:56,0:13,0:43,0 0/1:.:132:124,6:20,5:104,1 +chr8 144437095 . T G . PASS DP=103;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10209 GT:GQ:DP:AD:ADF:ADR 0/0:.:37:37,0:19,0:18,0 0/1:.:66:61,5:24,3:37,2 +chr9 34371544 . A C . PASS DP=83;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.091683 GT:GQ:DP:AD:ADF:ADR 0/0:.:30:30,0:12,0:18,0 0/1:.:53:46,5:27,1:19,4 +chr9 93257022 rs1843418763 T C . PASS DP=88;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11696;FREQ=dbGaP_PopFreq:1,3.13e-05;GENEINFO=WNK2:65268;SSR=0;SYN;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:30:30,0:18,0:12,0 0/1:.:58:53,5:39,1:14,4 +chr9 93257030 rs745449856 A C . PASS DP=91;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10193;FREQ=ExAC:1,1.163e-05,.|Korea1K:0.9984,0.001638,.|TOPMED:1,7.964e-06,.|dbGaP_PopFreq:0.9999,7.117e-05,0;GENEINFO=WNK2:65268;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:28:28,0:17,0:11,0 0/1:.:63:57,6:35,2:22,4 +chr9 122893029 . TA T . MinMMQSdiff DP=159;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.046021;INDEL GT:GQ:DP:AD:ADF:ADR 0/0:.:42:37,1:18,1:19,0 0/1:.:117:87,14:52,8:35,6 +chr9 128633818 . T C . PASS DP=133;SOMATIC;SS=2;SSC=12;GPV=1;SPV=0.055306 GT:GQ:DP:AD:ADF:ADR 0/0:.:39:39,0:20,0:19,0 0/1:.:94:85,8:51,1:34,7 +chr9 136763918 . A G . PASS DP=109;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.080707 GT:GQ:DP:AD:ADF:ADR 0/0:.:32:32,0:18,0:14,0 0/1:.:77:70,7:30,6:40,1 +chr9 137743352 . CT C . MinMMQSdiff DP=164;SOMATIC;SS=2;SSC=17;GPV=1;SPV=0.018344;INDEL GT:GQ:DP:AD:ADF:ADR 0/0:.:43:39,1:23,1:16,0 0/1:.:121:95,18:54,11:41,7 +chr10 11463685 . A G . PASS DP=102;SOMATIC;SS=2;SSC=16;GPV=1;SPV=0.0231 GT:GQ:DP:AD:ADF:ADR 0/0:.:41:40,1:23,1:17,0 0/1:.:61:51,10:18,9:33,1 +chr10 26697814 . A G . PASS DP=46;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11779 GT:GQ:DP:AD:ADF:ADR 0/0:.:18:18,0:6,0:12,0 0/1:.:28:23,4:8,3:15,1 +chr10 75108094 . T C . PASS DP=93;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.063155 GT:GQ:DP:AD:ADF:ADR 0/0:.:29:29,0:15,0:14,0 0/1:.:64:56,7:34,1:22,6 +chr10 119030064 rs1209333669 A C . PASS DP=29;SOMATIC;SS=2;SSC=19;GPV=1;SPV=0.010536;FREQ=TOPMED:1,.,2.389e-05|dbGaP_PopFreq:1,.,0;GENEINFO=NANOS1:340719;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:14:14,0:12,0:2,0 0/1:.:15:9,6:5,3:4,3 +chr11 6603418 . A G . PASS DP=78;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10724 GT:GQ:DP:AD:ADF:ADR 0/0:.:27:27,0:13,0:14,0 0/1:.:51:45,5:16,4:29,1 +chr11 32392004 . T TTGGGAGG . MinMMQSdiff DP=150;SOMATIC;SS=2;SSC=101;GPV=1;SPV=6.8811e-11;INDEL;LOF=(WT1|WT1|5|1.00) GT:GQ:DP:AD:ADF:ADR 0/0:.:41:41,0:31,0:10,0 0/1:.:109:52,55:27,27:25,28 +chr11 66333308 . A G . PASS DP=95;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.087528 GT:GQ:DP:AD:ADF:ADR 0/0:.:24:24,0:10,0:14,0 0/1:.:71:63,8:29,6:34,2 +chr11 66591673 rs1590825346 A C . PASS DP=114;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11476;FREQ=Korea1K:0.9967,0.003275;GENEINFO=CCS:9973|CCDC87:55231;NSM;R5;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:39:39,0:19,0:20,0 0/1:.:75:69,5:47,1:22,4 +chr12 39293733 . GA G . PASS DP=108;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.046488;INDEL GT:GQ:DP:AD:ADF:ADR 0/0:.:28:28,0:19,0:9,0 0/1:.:80:64,9:36,6:28,3 +chr12 52520086 . A G . PASS DP=83;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11591 GT:GQ:DP:AD:ADF:ADR 0/0:.:28:28,0:14,0:14,0 0/1:.:55:49,5:35,4:14,1 +chr12 113181030 . A C . PASS DP=116;SOMATIC;SS=2;SSC=95;GPV=1;SPV=2.8536e-10 GT:GQ:DP:AD:ADF:ADR 0/0:.:39:39,0:16,0:23,0 0/1:.:77:36,41:16,22:20,19 +chr12 122183296 . T G . PASS DP=60;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.046436;LOF=(LRRC43|LRRC43|2|0.50) GT:GQ:DP:AD:ADF:ADR 0/0:.:23:23,0:9,0:14,0 0/1:.:37:31,6:12,5:19,1 +chr14 91969289 . TA T . MinMMQSdiff DP=156;SOMATIC;SS=2;SSC=15;GPV=1;SPV=0.02796;INDEL GT:GQ:DP:AD:ADF:ADR 0/0:.:61:58,0:31,0:27,0 0/1:.:95:83,7:38,5:45,2 +chr15 41511296 . A G . PASS DP=43;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.1021 GT:GQ:DP:AD:ADF:ADR 0/0:.:15:15,0:5,0:10,0 0/1:.:28:23,5:10,3:13,2 +chr15 50609732 . TA T . MinMMQSdiff DP=191;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.078004;INDEL GT:GQ:DP:AD:ADF:ADR 0/0:.:51:49,0:23,0:26,0 0/1:.:140:126,8:64,5:62,3 +chr15 70891968 . T C . PASS DP=100;SOMATIC;SS=2;SSC=12;GPV=1;SPV=0.05157 GT:GQ:DP:AD:ADF:ADR 0/0:.:38:38,0:23,0:15,0 0/1:.:62:56,6:31,2:25,4 +chr16 662321 . T C . PASS DP=92;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11106 GT:GQ:DP:AD:ADF:ADR 0/0:.:32:32,0:20,0:12,0 0/1:.:60:55,5:29,2:26,3 +chr16 10907873 rs2039285618 A G . PASS DP=77;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.096829;FREQ=TOMMO:0.9996,0.000358;GENEINFO=CIITA:4261;INT;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:24:24,0:10,0:14,0 0/1:.:53:47,6:28,1:19,5 +chr16 30582843 rs1597148926 T G . PASS DP=71;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11095;FREQ=Korea1K:0.9973,0.002738;GENEINFO=ZNF785:146540;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:21:21,0:10,0:11,0 0/1:.:50:44,6:5,5:39,1 +chr16 30659613 rs2052429106 A G . PASS DP=20;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.068111;FREQ=dbGaP_PopFreq:1,0;GENEINFO=FBRS:64319;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:9:9,0:5,0:4,0 0/1:.:11:7,4:4,3:3,1 +chr16 57077971 rs762970987 A C . PASS DP=98;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.07847;FREQ=ExAC:1,.,8.548e-06|GnomAD_exomes:1,.,4.01e-06|dbGaP_PopFreq:1,0,.;GENEINFO=NLRC5:84166;NSM;R3;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:33:33,0:15,0:18,0 0/1:.:65:59,6:30,1:29,5 +chr16 67543151 . A G . PASS DP=99;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11701 GT:GQ:DP:AD:ADF:ADR 0/0:.:29:29,0:14,0:15,0 0/1:.:70:64,6:27,5:37,1 +chr16 84196276 . A C . PASS DP=68;SOMATIC;SS=2;SSC=14;GPV=1;SPV=0.03324 GT:GQ:DP:AD:ADF:ADR 0/0:.:25:25,0:16,0:9,0 0/1:.:43:36,7:10,5:26,2 +chr16 85657427 rs2052056269 T C . PASS DP=67;SOMATIC;SS=2;SSC=14;GPV=1;SPV=0.033048;FREQ=TOMMO:0.999,0.0009547;GENEINFO=GSE1:23199;NSM;R3;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:22:22,0:17,0:5,0 0/1:.:45:37,8:24,1:13,7 +chr17 7235658 rs1597560221 A C . PASS DP=148;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.072541;FREQ=Korea1K:0.9973,0.002729;GENEINFO=DVL2:1856|PHF23:79142;NSM;R5;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:45:45,0:21,0:24,0 0/1:.:103:95,7:62,1:33,6 +chr17 56834826 . T C . PASS DP=52;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11622 GT:GQ:DP:AD:ADF:ADR 0/0:.:21:21,0:16,0:5,0 0/1:.:31:27,4:15,2:12,2 +chr17 74525837 . A G . PASS DP=136;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10968 GT:GQ:DP:AD:ADF:ADR 0/0:.:36:36,0:20,0:16,0 0/1:.:100:93,7:40,6:53,1 +chr17 81665449 . A G . PASS DP=79;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.084997 GT:GQ:DP:AD:ADF:ADR 0/0:.:20:20,0:10,0:10,0 0/1:.:59:51,8:14,7:37,1 +chr18 23136360 . T G . PASS DP=31;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.048889 GT:GQ:DP:AD:ADF:ADR 0/0:.:15:14,0:4,0:10,0 0/1:.:16:10,4:6,3:4,1 +chr18 33943180 . TA T . MinMMQSdiff DP=120;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.079905;INDEL GT:GQ:DP:AD:ADF:ADR 0/0:.:39:39,0:29,0:10,0 0/1:.:81:71,6:37,5:34,1 +chr18 57436318 . A G . PASS DP=55;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.091832 GT:GQ:DP:AD:ADF:ADR 0/0:.:13:13,0:7,0:6,0 0/1:.:42:33,8:9,7:24,1 +chr19 3753833 . T C . PASS DP=49;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.042387 GT:GQ:DP:AD:ADF:ADR 0/0:.:12:12,0:6,0:6,0 0/1:.:37:27,10:18,1:9,9 +chr19 6375414 . T C . PASS DP=42;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11302 GT:GQ:DP:AD:ADF:ADR 0/0:.:17:17,0:9,0:8,0 0/1:.:25:21,4:10,1:11,3 +chr19 6375439 . A C . PASS DP=41;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11076 GT:GQ:DP:AD:ADF:ADR 0/0:.:15:15,0:8,0:7,0 0/1:.:26:18,4:8,1:10,3 +chr19 10092121 . A C . PASS DP=121;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10576 GT:GQ:DP:AD:ADF:ADR 0/0:.:37:37,0:16,0:21,0 0/1:.:84:78,6:51,1:27,5 +chr19 16878242 . A G . PASS DP=84;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.099575 GT:GQ:DP:AD:ADF:ADR 0/0:.:26:26,0:11,0:15,0 0/1:.:58:52,6:17,5:35,1 +chr19 17300950 rs1223479129 C G . PASS DP=87;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.049205;FREQ=GnomAD_exomes:1,4.023e-06,.|TOMMO:0.9992,.,0.0008354;GENEINFO=MRPL34:64981|ABHD8:79575;NSM;R5;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:29:29,0:14,0:15,0 0/1:.:58:50,7:15,6:35,1 +chr19 17830104 . T C . PASS DP=96;SOMATIC;SS=2;SSC=14;GPV=1;SPV=0.03365 GT:GQ:DP:AD:ADF:ADR 0/0:.:26:26,0:13,0:13,0 0/1:.:70:59,10:33,1:26,9 +chr19 39425108 . A C . PASS DP=91;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.047715 GT:GQ:DP:AD:ADF:ADR 0/0:.:31:31,0:13,0:18,0 0/1:.:60:53,7:27,3:26,4 +chr19 42225307 rs757193095 A C . PASS DP=61;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11061;FREQ=ExAC:0.9999,0.0001304;GENEINFO=ZNF526:116115;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:21:21,0:12,0:9,0 0/1:.:40:35,5:10,4:25,1 +chr19 45785825 . A C . PASS DP=65;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.063509 GT:GQ:DP:AD:ADF:ADR 0/0:.:23:23,0:11,0:12,0 0/1:.:42:36,6:21,2:15,4 +chr19 46787914 rs2055198734 T G . PASS DP=61;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11061;FREQ=TOMMO:0.9998,0.000179;GENEINFO=SLC1A5:6510;NSM;R5;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:21:21,0:13,0:8,0 0/1:.:40:35,5:21,4:14,1 +chr19 47754611 . A C . PASS DP=44;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10935 GT:GQ:DP:AD:ADF:ADR 0/0:.:15:15,0:8,0:7,0 0/1:.:29:24,5:8,4:16,1 +chr19 48837393 . T G . PASS DP=111;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.091093 GT:GQ:DP:AD:ADF:ADR 0/0:.:31:31,0:14,0:17,0 0/1:.:80:72,7:23,6:49,1 +chr19 49651647 rs7251334 A C . PASS DP=37;SOMATIC;SS=2;SSC=15;GPV=1;SPV=0.029941;FREQ=1000Genomes:0.003195,0.9968|ALSPAC:0.006746,0.9933|Estonian:0.009865,0.9901|ExAC:0.01316,0.9868|GENOME_DK:0.075,0.925|GnomAD:0.009591,0.9904|GnomAD_exomes:0.01297,0.987|KOREAN:0.0003544,0.9996|Korea1K:0,1|NorthernSweden:0.01333,0.9867|Qatari:0.009259,0.9907|SGDP_PRJ:0.00369,0.9963|Siberian:0,1|TOMMO:5.996e-05,0.9999|TOPMED:0.009007,0.991|TWINSUK:0.002697,0.9973|dbGaP_PopFreq:0.01097,0.989;GENEINFO=SCAF1:58506;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:10:9,1:4,1:5,0 0/1:.:27:13,13:7,7:6,6 +chr20 36436128 . A G . PASS DP=80;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.085947 GT:GQ:DP:AD:ADF:ADR 0/0:.:26:26,0:8,0:18,0 0/1:.:54:48,6:13,5:35,1 +chr20 36436160 . A G . PASS DP=85;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11645 GT:GQ:DP:AD:ADF:ADR 0/0:.:29:29,0:12,0:17,0 0/1:.:56:51,5:21,4:30,1 +chr20 38926705 . A G . PASS DP=32;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10779 GT:GQ:DP:AD:ADF:ADR 0/0:.:13:13,0:6,0:7,0 0/1:.:19:15,4:2,3:13,1 +chr20 49850763 . G GT . MinMMQSdiff DP=138;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10754;INDEL;LOF=(SLC9A8|SLC9A8|6|0.17) GT:GQ:DP:AD:ADF:ADR 0/0:.:37:36,0:20,0:16,0 0/1:.:101:92,7:41,2:51,5 +chr20 58470723 rs780513473 T C . PASS DP=68;SOMATIC;SS=2;SSC=15;GPV=1;SPV=0.027829;FREQ=ExAC:0.9997,0.0002659|Korea1K:0.9961,0.003855;GENEINFO=APCDD1L:164284;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:26:26,0:12,0:14,0 0/1:.:42:35,7:11,1:24,6 +chr20 63962289 . A G . PASS DP=119;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.074509 GT:GQ:DP:AD:ADF:ADR 0/0:.:32:32,0:12,0:20,0 0/1:.:87:79,8:28,7:51,1 +chr21 44294402 . A G . PASS DP=39;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.093821 GT:GQ:DP:AD:ADF:ADR 0/0:.:10:10,0:9,0:1,0 0/1:.:29:21,7:20,7:1,0 +chr21 46391311 . A G . PASS DP=98;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.07847 GT:GQ:DP:AD:ADF:ADR 0/0:.:33:33,0:13,0:20,0 0/1:.:65:59,6:19,4:40,2 +chr22 21642940 rs779759705 A G . PASS DP=54;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.086849;FREQ=ExAC:0.9999,7.462e-05|GnomAD:1,7.143e-06|GnomAD_exomes:1,2.219e-05|TOPMED:1,7.556e-06|dbGaP_PopFreq:1,0;GENEINFO=SDF2L1:23753;NSM;SSR=0;VC=SNV GT:GQ:DP:AD:ADF:ADR 0/0:.:15:15,0:9,0:6,0 0/1:.:39:32,7:16,6:16,1 +chr22 24095973 . A G . PASS DP=135;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.11972 GT:GQ:DP:AD:ADF:ADR 0/0:.:46:46,0:16,0:30,0 0/1:.:89:84,5:29,4:55,1 +chr22 29050610 . T C . PASS DP=75;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.089227 GT:GQ:DP:AD:ADF:ADR 0/0:.:21:21,0:14,0:7,0 0/1:.:54:47,7:36,1:11,6 +chr22 37373680 . T C . PASS DP=91;SOMATIC;SS=2;SSC=9;GPV=1;SPV=0.10913 GT:GQ:DP:AD:ADF:ADR 0/0:.:27:27,0:15,0:12,0 0/1:.:64:57,6:34,4:23,2 +chrX 13713103 . CA C . MinMMQSdiff DP=118;SOMATIC;SS=2;SSC=12;GPV=1;SPV=0.05176;INDEL GT:GQ:DP:AD:ADF:ADR 0/0:.:39:32,0:16,0:16,0 0/1:.:79:67,8:28,6:39,2 +chrX 22111531 . T C . PASS DP=154;SOMATIC;SS=2;SSC=13;GPV=1;SPV=0.048459 GT:GQ:DP:AD:ADF:ADR 0/0:.:53:53,0:31,0:22,0 0/1:.:101:94,7:42,6:52,1 +chrX 71132767 . C CCTCTT . MinMMQSdiff DP=105;SOMATIC;SS=2;SSC=14;GPV=1;SPV=0.035112;INDEL GT:GQ:DP:AD:ADF:ADR 0/0:.:31:27,1:8,0:19,1 0/1:.:74:52,13:24,8:28,5 +chrX 75431524 . T TA . PASS DP=201;SOMATIC;SS=2;SSC=11;GPV=1;SPV=0.066007;INDEL GT:GQ:DP:AD:ADF:ADR 0/0:.:58:54,0:25,0:29,0 0/1:.:143:129,8:61,3:68,5 +chrX 153647994 . A G . PASS DP=31;SOMATIC;SS=2;SSC=10;GPV=1;SPV=0.097251 GT:GQ:DP:AD:ADF:ADR 0/0:.:13:13,0:5,0:8,0 0/1:.:18:14,4:4,3:10,1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/varscan_vaf.py Mon Nov 28 21:59:34 2022 +0000 @@ -0,0 +1,56 @@ +#!/usr/bin/python3 + +import argparse + + +def Parser(): + the_parser = argparse.ArgumentParser() + the_parser.add_argument( + '--input', action="store", type=str, + help="varscan vcf file with normal and tumor genotypes \ + (columns 10 and 11)") + the_parser.add_argument( + '--output', action="store", type=str, + help="vcf with computed VAFs") + args = the_parser.parse_args() + return args + + +def main(input, output): + with open(input, 'r') as f: + myinput = f.read() + mylines = myinput.split('\n') + entete = [i for i in mylines[:-1] if i[0] == '#'] + variant = [i for i in mylines[:-1] if i[0] != '#'] + out = open(output, 'w') + out.write('\n'.join(entete[:-1]) + '\n') + out.write('##FORMAT=<ID=VAF,Number=R,Type=float,Description="Variant' + 'Allele Frequency">\n') + out.write(entete[-1] + '\n') + for i in variant: + fields = i.split('\t')[9:11] + af_normal = fields[0].split(':')[3] + vac_normal = af_normal.split(',') + af_tumor = fields[1].split(':')[3] + vac_tumor = af_tumor.split(',') + vaf_normal = int( + vac_normal[1]) / (int(vac_normal[0]) + int(vac_normal[1])) + vaf_tumor = int( + vac_tumor[1]) / (int(vac_tumor[0]) + int(vac_tumor[1])) + normal_list = fields[0].split(':') + normal_list.append(f'{vaf_normal:.3f}') + tumor_list = fields[1].split(':') + tumor_list.append(f'{vaf_tumor:.3f}') + normal_string = ':'.join(normal_list) + tumor_string = ':'.join(tumor_list) + fields = i.split('\t')[0:9] + fields[8] += ':VAF' + fields.append(normal_string) + fields.append(tumor_string) + out.write('\t'.join(fields) + '\n') + out.close() + + +if __name__ == "__main__": + args = Parser() + main(args.input, args.output)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/varscan_vaf.xml Mon Nov 28 21:59:34 2022 +0000 @@ -0,0 +1,55 @@ +<tool id="varscan_vaf" name="Compute VAFs from varscan VCFs" version="0.1"> + <description /> + <requirements> + <requirement type="package" version="3.7.6">python</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python $__tool_directory__/varscan_vaf.py + --input '$input' + --output '$output' + ]]></command> + <inputs> + <param format="vcf" label="VCF file" name="input" type="data" + help="a VCF file generated by somatic varscan (normal and tumor genotype), + or having a compatible FORMAT column (9th column)"/> + </inputs> + <outputs> + <data format="vcf" name="output" label="VCF with computed VAFs" /> + </outputs> + <tests> + <test> + <param ftype="vcf" name="input" value="vcf_1.vcf" /> + <output file="computed_VAFs_1.vcf" name="output" /> + </test> + <test> + <param ftype="vcf" name="input" value="vcf_2.vcf" /> + <output file="computed_VAFs_2.vcf" name="output" /> + </test> + </tests> + <help> + +**What it does** + ++ Computes VAFs in normal and tumor samples. ++ Uses AD field of genotypes (##FORMAT ID=AD), composed of REF and ALT Read depths, separated by a comma. ++ A new genotype field 'VAF" (##FORMAT IF=VAF) is generated ++ VAF = AD(ALT) / (AD(ALT) + AD(REF)) + +------- + +**Inputs** + +1. A somatic varscan VCF with AD field in third position. +2. The AD field must be composed of two integers separated by a comma. + +------- + +**Output** + ++ A VCF file ++ A line '##FORMAT=<ID=VAF,Number=R,Type=float,Description="Variant Allele Frequency">' is added in the header ++ The VAF value is added in both normal and tumor genotype column, as a last field + + </help> + <citations /> +</tool>