| Previous changeset 2:c15d9049ab81 (2018-11-14) |
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Commit message:
Uploaded |
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added:
ctat_mutations.xml test-data/reads_1.fastq.gz test-data/reads_2.fastq.gz test-data/varcalling.outdir/annotated_min_filtered.vcf.gz test-data/varcalling.outdir/cancer.tab test-data/varcalling.outdir/cancer.vcf test-data/varcalling.outdir/misc/recalibrated.bai test-data/varcalling.outdir/misc/recalibrated.bam test-data/varcalling.outdir/mutation_inspector.json test-data/varcalling.outdir/variants.vcf test-data/varcalling.outdir/variants.vcf.idx test-data/varcalling.outdir/variants_initial_filtering_clean_snp_RNAedit.vcf_snpeff_updated.vcf.gz tool-data/cravat_tissues.loc.sample tool-data/ctat_genome_resource_libs.loc.sample tool_data_table_conf.xml.sample |
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removed:
ctat_mutations-7cf8f5889a4d/ctat_mutations.xml ctat_mutations-7cf8f5889a4d/test-data/reads_1.fastq.gz ctat_mutations-7cf8f5889a4d/test-data/reads_2.fastq.gz ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/annotated_min_filtered.vcf.gz ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/cancer.tab ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/cancer.vcf ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/misc/recalibrated.bai ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/misc/recalibrated.bam ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/mutation_inspector.json ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/variants.vcf ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/variants.vcf.idx ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/variants_initial_filtering_clean_snp_RNAedit.vcf_snpeff_updated.vcf.gz ctat_mutations-7cf8f5889a4d/tool-data/cravat_tissues.loc.sample ctat_mutations-7cf8f5889a4d/tool-data/ctat_genome_resource_libs.loc.sample ctat_mutations-7cf8f5889a4d/tool_data_table_conf.xml.sample |
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| diff -r c15d9049ab81 -r b591b35283e4 ctat_mutations-7cf8f5889a4d/ctat_mutations.xml --- a/ctat_mutations-7cf8f5889a4d/ctat_mutations.xml Wed Nov 14 12:20:23 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,68 +0,0 @@ -<tool id="ctat_mutations" name="ctat_mutations" version="1.0.0" profile="17.05"> - <description>Mutation Pipeline for calling SNPs and variants</description> - <requirements> - <requirement type="package" version="2.0.1">ctat-mutations</requirement> - </requirements> - <command detect_errors="default"> - <![CDATA[ - ctat_mutations \ - --plot \ - --out_dir varcalling.outdir \ - --threads 8 \ - --variant_filtering_mode GATK \ - --left "$left" \ - --right "$right" \ - --genome_lib_dir "${genome_resource_lib.fields.path}" \ - --variant_call_mode GATK \ - --tissue_type "$tissue_type" \ - --email "$cravat_email" - ]]> - </command> - <inputs> - <param format="fastq" name="left" type="data" label="Left/Forward strand reads" help="Left read"/> - <param format="fastq" name="right" type="data" label="Right/Reverse strand reads" help="Right read"/> - <param name="tissue_type" type="select" label="Select a pathology" help="If you don't know, just choose 'General Purpose'"> - <options from_data_table="ctat_cravat_tissues"> - <filter type="sort_by" column="1"/> - <validator type="no_options" message="No indexes are available for the selected input dataset"/> - </options> - </param> - <param name="genome_resource_lib" type="select" label="Select a reference genome"> - <options from_data_table="ctat_genome_resource_libs"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No indexes are available" /> - </options> - </param> - <param name="cravat_email" type="text" label="CRAVAT email" help="CRAVAT registered email id"/> - <section name="adv" title="This service uses the GATK4. GATK4 is licensed by the Broad Institute and is made available to academic users of this service for non-commercial use only. The full text of the license is available here: https://www.broadinstitute.org/gatk/about/license.html. For more information about GATK and full documentation, please visit the GATK website: https://www.broadinstitute.org." expanded="False"> - </section> - </inputs> - <outputs> - <data format="tabular" name="cancertab" label="${tool.name} on ${on_string}: Cancer Tab" from_work_dir="varcalling.outdir/cancer.tab"/> - <data format="vcf" name="cancerVariants" label="${tool.name} on ${on_string}: Cancer VCF" from_work_dir="varcalling.outdir/cancer.vcf"/> - <data format="vcf" name="allVariants" label="${tool.name} on ${on_string}: All Variants VCF" from_work_dir="varcalling.outdir/variants.vcf"/> - <data format="bam" name="bamfile" label="Bam used in haplotype calling" from_work_dir="varcalling.outdir/misc/recalibrated.bam"/> - <data format="txt" name="cravat" label="Annotated (lightly filtered) VCF file" from_work_dir="varcalling.outdir/variants_initial_filtering_clean_snp_RNAedit.vcf_snpeff_updated.vcf.gz"/> - </outputs> - <tests> - <test> - <param name="left" value="reads_1.fastq.gz"/> - <param name="right" value="reads_2.fastq.gz"/> - <param name="tissue_type" value="Other"/> - <output name="cancertab" file="varcalling.outdir/cancer.tab" /> - <output name="cancerVariants" file="varcalling.outdir/cancer.vcf" /> - <output name="allVariants" file="varcalling.outdir/variants.vcf" /> - <output name="bamfile" file="varcalling.outdir/misc/recalibrated.bam" /> - <output name="cravat" file="varcalling.outdir/variants_initial_filtering_clean_snp_RNAedit.vcf_snpeff_updated.vcf.gz"/> - </test> - </tests> - <help> - -.. class:: warningmark - -Mutation detection in RNA-Seq highlights the GATK Best Practices in RNA-Seq variant calling, several sources of variant annotation, and filtering based on CRAVAT. - - </help> - <citations> - </citations> -</tool> |
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| diff -r c15d9049ab81 -r b591b35283e4 ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/annotated_min_filtered.vcf.gz |
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| diff -r c15d9049ab81 -r b591b35283e4 ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/cancer.tab --- a/ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/cancer.tab Wed Nov 14 12:20:23 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,14 +0,0 @@ -CHROM POS REF ALT GENE DP QUAL MQ SAO NSF NSM NSN TUMOR TISSUE COSMIC_ID KGPROD RS PMC CHASM_PVALUE CHASM_FDR VEST_PVALUE VEST_FDR -chr5 474989 A G LOC100288152,SLC9A3 4 96.03 60 NA NA NA NA carcinoma_--_NS urinary_tract COSM4006021 NA NA NA 0.1114 0.2 0.96802 1 -chr5 181224474 G A TRIM41 45 349.77 60 NA NA NA NA NA NA NA NA NA NA 0.0694 0.15 0.48052 1 -chr8 143923759 G A PLEC 66 838.77 60 NA NA NA NA carcinoma_--_adenocarcinoma large_intestine COSM3750086 NA NA NA 0.0344 0.1 0.84202 1 -chr12 56420869 G A TIMELESS 48 384.77 60 NA NA NA NA carcinoma_--_adenocarcinoma large_intestine COSM3753397 NA NA NA 0.0744 0.15 0.18439 0.95 -chr17 7673767 C T TP53 61 1848.77 60 NA NA NA NA Ewings_sarcoma-peripheral_primitive_neuroectodermal_tumour_--_NS bone COSM3717625 NA NA NA 0 0.05 0.01447 0.15 -chr17 7676154 G C TP53 80 2161.77 60 NA NA NA NA haematopoietic_neoplasm_--_acute_myeloid_leukaemia haematopoietic_and_lymphoid_tissue COSM3766193 NA NA NA 0.087 0.15 0.52717 1 -chr17 43071077 T C BRCA1 4 92.03 60 NA NA NA NA haematopoietic_neoplasm_--_acute_myeloid_leukaemia haematopoietic_and_lymphoid_tissue COSM3755560 NA NA NA 0.0372 0.1 0.3446 1 -chr17 43091983 T C BRCA1 4 84.03 60 NA NA NA NA haemangioblastoma_--_NS soft_tissue COSM3755561 NA NA NA 0.0002 0.05 0.64447 1 -chr17 43092919 G A BRCA1 2 33.74 60 NA NA NA NA carcinoma_--_NS prostate COSM3755564 NA NA NA 0.0004 0.05 0.33539 1 -chr17 43093454 C T BRCA1 11 425.77 60 NA NA NA NA rhabdomyosarcoma_--_embryonal soft_tissue COSM4989394 NA NA NA 0.0014 0.05 0.51068 1 -chr19 39177761 G C PAK4 106 1134.77 60 NA NA NA NA NA NA NA NA NA NA 0.0004 0.05 0.01093 0.15 -chr19 47271515 T C CCDC9 12 336.77 60 NA NA NA NA haematopoietic_neoplasm_--_acute_myeloid_leukaemia haematopoietic_and_lymphoid_tissue COSM3721172 NA NA NA 0.093 0.15 0.97622 1 -chr20 46687147 C T TP53RK 26 423.77 60 NA NA NA NA carcinoma_--_ductal_carcinoma pancreas COSM3758608 NA NA NA 0.0834 0.15 0.88584 1 |
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| diff -r c15d9049ab81 -r b591b35283e4 ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/cancer.vcf --- a/ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/cancer.vcf Wed Nov 14 12:20:23 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,87 +0,0 @@\n-##fileformat=VCFv4.2\n-##FILTER=<ID=PASS,Description="All filters passed">\n-##FILTER=<ID=FS,Description="FS > 30.0">\n-##FILTER=<ID=LowQual,Description="Low quality">\n-##FILTER=<ID=QD,Description="QD < 2.0">\n-##FILTER=<ID=SnpCluster,Description="SNPs found in clusters">\n-##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n-##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n-##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --recover-dangling-heads true --dont-use-soft-clipped-bases true --standard-min-confidence-threshold-for-calling 20.0 --output /broad/hptmp/bankapur/full_mut/varcalling.outdir/variants.vcf --input /broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/recalibrated.bam --reference /seq/regev_genome_portal/RESOURCES/CTAT_GENOME_LIB/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa --emit-ref-confidence NONE --gvcf-gq-bands 1 --gvcf-gq-bands 2 --gvcf-gq-bands 3 --gvcf-gq-bands 4 --gvcf-gq-bands 5 --gvcf-gq-bands 6 --gvcf-gq-bands 7 --gvcf-gq-bands 8 --gvcf-gq-bands 9 --gvcf-gq-bands 10 --gvcf-gq-bands 11 --gvcf-gq-bands 12 --gvcf-gq-bands 13 --gvcf-gq-bands 14 --gvcf-gq-bands 15 --gvcf-gq-bands 16 --gvcf-gq-bands 17 --gvcf-gq-bands 18 --gvcf-gq-bands 19 --gvcf-gq-bands 20 --gvcf-gq-bands 21 --gvcf-gq-bands 22 --gvcf-gq-bands 23 --gvcf-gq-bands 24 --gvcf-gq-bands 25 --gvcf-gq-bands 26 --gvcf-gq-bands 27 --gvcf-gq-bands 28 --gvcf-gq-bands 29 --gvcf-gq-bands 30 --gvcf-gq-bands 31 --gvcf-gq-bands 32 --gvcf-gq-bands 33 --gvcf-gq-bands 34 --gvcf-gq-bands 35 --gvcf-gq-bands 36 --gvcf-gq-bands 37 --gvcf-gq-bands 38 --gvcf-gq-bands 39 --gvcf-gq-bands 40 --gvcf-gq-bands 41 --gvcf-gq-bands 42 --gvcf-gq-bands 43 --gvcf-gq-bands 44 --gvcf-gq-bands 45 --gvcf-gq-bands 46 --gvcf-gq-bands 47 --gvcf-gq-bands 48 --gvcf-gq-bands 49 --gvcf-gq-bands 50 --gvcf-gq-bands 51 --gvcf-gq-bands 52 --gvcf-gq-bands 53 --gvcf-gq-bands 54 --gvcf-gq-bands 55 --gvcf-gq-bands 56 --gvcf-gq-bands 57 --gvcf-gq-bands 58 --gvcf-gq-bands 59 --gvcf-gq-bands 60 --gvcf-gq-bands 70 --gvcf-gq-bands 80 --gvcf-gq-bands 90 --gvcf-gq-bands 99 --indel-size-to-eliminate-in-ref-model 10 --use-alleles-trigger false --disable-optimizations false --just-determine-active-regions false --dont-genotype false --max-mnp-distance 0 --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --do-not-recover-dangling-branches false --min-dangling-branch-length 4 --consensus false --max-num-haplotypes-in-population 128 --error-correct-kmers false --min-pruning 2 --debug-graph-transformations false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --use-new-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --max-alternate-alleles 6 '..b'MLEAF=1;MQ=60;QD=16.87;SOR=2.303;ANN=A|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007300.3|Coding|10/24|c.2612C>T|p.Pro871Leu|2844/7270|2612/5655|871/1884||,A|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007297.3|Coding|9/22|c.2471C>T|p.Pro824Leu|2752/7115|2471/5451|824/1816||,A|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007294.3|Coding|10/23|c.2612C>T|p.Pro871Leu|2844/7207|2612/5592|871/1863||,A|intron_variant|MODIFIER|BRCA1|BRCA1|transcript|NM_007298.3|Coding|9/21|c.787+1825C>T||||||,A|intron_variant|MODIFIER|BRCA1|BRCA1|transcript|NM_007299.3|Coding|10/21|c.787+1825C>T||||||,A|non_coding_exon_variant|MODIFIER|BRCA1|BRCA1|transcript|NR_027676.1|Noncoding|10/23|n.2748C>T||||||;COSMIC_ID=COSM3755564;TISSUE=prostate;TUMOR=carcinoma_--_NS;FATHMM=NEUTRAL;SOMATIC=Confirmed_somatic_variant;CHASM_PVALUE=0.0004;CHASM_FDR=0.05;VEST_PVALUE=0.33539;VEST_FDR=1\tGT:AD:DP:GQ:PL\t1/1:0,2:2:6:61,6,0\n-chr17\t43093454\t.\tC\tT\t425.77\tPASS\tGENE=BRCA1;AC=2;AF=1;AN=2;DP=11;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;QD=31.78;SOR=1.27;ANN=T|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007300.3|Coding|10/24|c.2077G>A|p.Asp693Asn|2309/7270|2077/5655|693/1884||,T|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007297.3|Coding|9/22|c.1936G>A|p.Asp646Asn|2217/7115|1936/5451|646/1816||,T|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007294.3|Coding|10/23|c.2077G>A|p.Asp693Asn|2309/7207|2077/5592|693/1863||,T|intron_variant|MODIFIER|BRCA1|BRCA1|transcript|NM_007298.3|Coding|9/21|c.787+1290G>A||||||,T|intron_variant|MODIFIER|BRCA1|BRCA1|transcript|NM_007299.3|Coding|10/21|c.787+1290G>A||||||,T|non_coding_exon_variant|MODIFIER|BRCA1|BRCA1|transcript|NR_027676.1|Noncoding|10/23|n.2213G>A||||||;COSMIC_ID=COSM4989394;TISSUE=soft_tissue;TUMOR=rhabdomyosarcoma_--_embryonal;FATHMM=NEUTRAL;SOMATIC=Reported_in_another_cancer_sample_as_somatic;CHASM_PVALUE=0.0014;CHASM_FDR=0.05;VEST_PVALUE=0.51068;VEST_FDR=1\tGT:AD:DP:GQ:PL\t1/1:0,11:11:33:454,33,0\n-chr19\t39177761\t.\tG\tC\t1134.77\tPASS\tGENE=PAK4;AC=1;AF=0.5;AN=2;BaseQRankSum=2.258;DP=106;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=60;MQRankSum=0;QD=10.71;ReadPosRankSum=1.397;SOR=0.654;ANN=C|missense_variant|MODERATE|PAK4|PAK4|transcript|NM_001014831.2|Coding|10/11|c.1572G>C|p.Met524Ile|2033/3064|1572/1776|524/591||,C|missense_variant|MODERATE|PAK4|PAK4|transcript|NM_001014832.1|Coding|8/9|c.1572G>C|p.Met524Ile|1734/2765|1572/1776|524/591||,C|missense_variant|MODERATE|PAK4|PAK4|transcript|NM_001014834.2|Coding|7/8|c.1113G>C|p.Met371Ile|1275/2306|1113/1317|371/438||,C|missense_variant|MODERATE|PAK4|PAK4|transcript|NM_001014835.1|Coding|8/9|c.1113G>C|p.Met371Ile|1348/2379|1113/1317|371/438||,C|missense_variant|MODERATE|PAK4|PAK4|transcript|NM_005884.3|Coding|9/10|c.1572G>C|p.Met524Ile|1807/2838|1572/1776|524/591||;CHASM_PVALUE=0.0004;CHASM_FDR=0.05;VEST_PVALUE=0.01093;VEST_FDR=0.15\tGT:AD:DP:GQ:PL\t0/1:58,48:106:99:1163,0,1435\n-chr19\t47271515\t.\tT\tC\t336.77\tPASS\tGENE=CCDC9;AC=2;AF=1;AN=2;DP=12;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;QD=28.06;SOR=2.67;ANN=C|missense_variant|MODERATE|CCDC9|CCDC9|transcript|NM_015603.2|Coding|12/12|c.1433T>C|p.Leu478Pro|1640/2078|1433/1596|478/531||;COSMIC_ID=COSM3721172;TISSUE=haematopoietic_and_lymphoid_tissue;TUMOR=haematopoietic_neoplasm_--_acute_myeloid_leukaemia;FATHMM=NEUTRAL;SOMATIC=Confirmed_somatic_variant;CHASM_PVALUE=0.093;CHASM_FDR=0.15;VEST_PVALUE=0.97622;VEST_FDR=1\tGT:AD:DP:GQ:PL\t1/1:0,12:12:36:365,36,0\n-chr20\t46687147\t.\tC\tT\t423.77\tPASS\tGENE=TP53RK;AC=1;AF=0.5;AN=2;BaseQRankSum=-0.26;DP=26;ExcessHet=3.0103;FS=1.657;MLEAC=1;MLEAF=0.5;MQ=60;MQRankSum=0;QD=16.3;ReadPosRankSum=1.395;SOR=1.179;ANN=T|missense_variant|MODERATE|TP53RK|TP53RK|transcript|NM_033550.3|Coding|2/2|c.368G>A|p.Arg123Gln|591/3373|368/762|123/253||;COSMIC_ID=COSM3758608;TISSUE=pancreas;TUMOR=carcinoma_--_ductal_carcinoma;FATHMM=PATHOGENIC;SOMATIC=Confirmed_somatic_variant;CHASM_PVALUE=0.0834;CHASM_FDR=0.15;VEST_PVALUE=0.88584;VEST_FDR=1\tGT:AD:DP:GQ:PL\t0/1:8,18:26:99:452,0,165\n' 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| diff -r c15d9049ab81 -r b591b35283e4 ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/mutation_inspector.json --- a/ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/mutation_inspector.json Wed Nov 14 12:20:23 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,321 +0,0 @@\n-{\n- "BAM": "/broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/recalibrated.bam", \n- "BAM_INDEX": "/broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/recalibrated.bai", \n- "BED": "/seq/regev_genome_portal/RESOURCES/CTAT_GENOME_LIB/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ctat_mutation_lib/refGene.sort.bed", \n- "BED_INDEX": "/seq/regev_genome_portal/RESOURCES/CTAT_GENOME_LIB/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ctat_mutation_lib/refGene.sort.bed.idx", \n- "SAMPLE": "varcalling.outdir", \n- "SNV": [\n- {\n- "ALT": "G", \n- "CHASM_FDR": "0.2", \n- "CHASM_PVALUE": "0.1114", \n- "CHROM": "chr5", \n- "COSMIC_ID": "COSM4006021", \n- "DP": "4", \n- "GENE": "LOC100288152,SLC9A3", \n- "KGPROD": "NA", \n- "MQ": "60", \n- "NSF": "NA", \n- "NSM": "NA", \n- "NSN": "NA", \n- "PMC": "NA", \n- "POS": "474989", \n- "QUAL": "96.03", \n- "REF": "A", \n- "RS": "NA", \n- "SAO": "NA", \n- "TISSUE": "urinary_tract", \n- "TUMOR": "carcinoma_--_NS", \n- "VEST_FDR": "1", \n- "VEST_PVALUE": "0.96802"\n- }, \n- {\n- "ALT": "A", \n- "CHASM_FDR": "0.15", \n- "CHASM_PVALUE": "0.0694", \n- "CHROM": "chr5", \n- "COSMIC_ID": "NA", \n- "DP": "45", \n- "GENE": "TRIM41", \n- "KGPROD": "NA", \n- "MQ": "60", \n- "NSF": "NA", \n- "NSM": "NA", \n- "NSN": "NA", \n- "PMC": "NA", \n- "POS": "181224474", \n- "QUAL": "349.77", \n- "REF": "G", \n- "RS": "NA", \n- "SAO": "NA", \n- "TISSUE": "NA", \n- "TUMOR": "NA", \n- "VEST_FDR": "1", \n- "VEST_PVALUE": "0.48052"\n- }, \n- {\n- "ALT": "A", \n- "CHASM_FDR": "0.1", \n- "CHASM_PVALUE": "0.0344", \n- "CHROM": "chr8", \n- "COSMIC_ID": "COSM3750086", \n- "DP": "66", \n- "GENE": "PLEC", \n- "KGPROD": "NA", \n- "MQ": "60", \n- "NSF": "NA", \n- "NSM": "NA", \n- "NSN": "NA", \n- "PMC": "NA", \n- "POS": "143923759", \n- "QUAL": "838.77", \n- "REF": "G", \n- "RS": "NA", \n- "SAO": "NA", \n- "TISSUE": "large_intestine", \n- "TUMOR": "carcinoma_--_adenocarcinoma", \n- "VEST_FDR": "1", \n- "VEST_PVALUE": "0.84202"\n- }, \n- {\n- "ALT": "A", \n- "CHASM_FDR": "0.15", \n- "CHASM_PVALUE": "0.0744", \n- "CHROM": "chr12", \n- "COSMIC_ID": "COSM3753397", \n- "DP": "48", \n- "GENE": "TIMELESS", \n- "KGPROD": "NA", \n- "MQ": "60", \n- "NSF": "NA", \n- "NSM": "NA", \n- "NSN": "NA", \n- "PMC": "NA", \n- "POS": "56420869", \n- "QUAL": "384.77", \n- "REF": "G", \n- "RS": "NA", \n- "SAO": "NA", \n- "TISSUE": "large_intestine", \n- "TUMOR": "carcinoma_--_adenocarcinoma", \n- "VEST_FDR": "0.95", \n- "VEST_PVALUE": "0.18439"\n- }, \n- {\n- "ALT": "T", \n- "CHASM_FDR": "0.05", \n- "CHASM_PVALUE": "0", \n- "CHROM": "chr17", \n- "COSMIC_ID": "COSM3717625", \n- "DP": "61", \n- "GENE": "TP53", \n- "KGPROD": "NA", \n- "MQ": "60", \n- "NSF": "NA", \n- "NSM": "NA", \n- "NSN": "NA", \n- "PMC": "NA", \n- "POS": "7673767", \n- "QUAL": "1848.77", \n- "REF": "C", \n- "RS": "NA", \n- "SAO": "NA", \n- "TISSUE": "bone", \n- "TUMOR": "Ewings_sarcoma-peripheral_primitive_neuroectodermal_tumour_--_NS", \n- "VEST_FDR": "0.15", \n- "VEST_PVALUE": "0.01447"\n- }, \n- {\n- "ALT": "C", \n- "CHASM_FDR": "0.15", \n- "CHASM_PVALUE": "0.087", \n- "CHROM": "chr17", \n- "COSMIC_ID": "COSM3766193", \n- "DP": "80", \n- "GENE": "TP53", \n- "KGPROD": "NA", \n- "MQ": "60", \n- "NSF": "NA", \n- "NSM": "NA", \n- "NSN": "NA", \n- "PMC": "NA", \n- "POS": "7676154", \n- "QUAL": "2161.77", \n- "REF": "G", \n- "RS": "NA", \n- "SAO": "NA", \n- "TISSUE": "haematopoietic_and_lymphoid_tissue", \n- "TUMOR":'..b'"4", \n- "GENE": "BRCA1", \n- "KGPROD": "NA", \n- "MQ": "60", \n- "NSF": "NA", \n- "NSM": "NA", \n- "NSN": "NA", \n- "PMC": "NA", \n- "POS": "43071077", \n- "QUAL": "92.03", \n- "REF": "T", \n- "RS": "NA", \n- "SAO": "NA", \n- "TISSUE": "haematopoietic_and_lymphoid_tissue", \n- "TUMOR": "haematopoietic_neoplasm_--_acute_myeloid_leukaemia", \n- "VEST_FDR": "1", \n- "VEST_PVALUE": "0.3446"\n- }, \n- {\n- "ALT": "C", \n- "CHASM_FDR": "0.05", \n- "CHASM_PVALUE": "0.0002", \n- "CHROM": "chr17", \n- "COSMIC_ID": "COSM3755561", \n- "DP": "4", \n- "GENE": "BRCA1", \n- "KGPROD": "NA", \n- "MQ": "60", \n- "NSF": "NA", \n- "NSM": "NA", \n- "NSN": "NA", \n- "PMC": "NA", \n- "POS": "43091983", \n- "QUAL": "84.03", \n- "REF": "T", \n- "RS": "NA", \n- "SAO": "NA", \n- "TISSUE": "soft_tissue", \n- "TUMOR": "haemangioblastoma_--_NS", \n- "VEST_FDR": "1", \n- "VEST_PVALUE": "0.64447"\n- }, \n- {\n- "ALT": "A", \n- "CHASM_FDR": "0.05", \n- "CHASM_PVALUE": "0.0004", \n- "CHROM": "chr17", \n- "COSMIC_ID": "COSM3755564", \n- "DP": "2", \n- "GENE": "BRCA1", \n- "KGPROD": "NA", \n- "MQ": "60", \n- "NSF": "NA", \n- "NSM": "NA", \n- "NSN": "NA", \n- "PMC": "NA", \n- "POS": "43092919", \n- "QUAL": "33.74", \n- "REF": "G", \n- "RS": "NA", \n- "SAO": "NA", \n- "TISSUE": "prostate", \n- "TUMOR": "carcinoma_--_NS", \n- "VEST_FDR": "1", \n- "VEST_PVALUE": "0.33539"\n- }, \n- {\n- "ALT": "T", \n- "CHASM_FDR": "0.05", \n- "CHASM_PVALUE": "0.0014", \n- "CHROM": "chr17", \n- "COSMIC_ID": "COSM4989394", \n- "DP": "11", \n- "GENE": "BRCA1", \n- "KGPROD": "NA", \n- "MQ": "60", \n- "NSF": "NA", \n- "NSM": "NA", \n- "NSN": "NA", \n- "PMC": "NA", \n- "POS": "43093454", \n- "QUAL": "425.77", \n- "REF": "C", \n- "RS": "NA", \n- "SAO": "NA", \n- "TISSUE": "soft_tissue", \n- "TUMOR": "rhabdomyosarcoma_--_embryonal", \n- "VEST_FDR": "1", \n- "VEST_PVALUE": "0.51068"\n- }, \n- {\n- "ALT": "C", \n- "CHASM_FDR": "0.05", \n- "CHASM_PVALUE": "0.0004", \n- "CHROM": "chr19", \n- "COSMIC_ID": "NA", \n- "DP": "106", \n- "GENE": "PAK4", \n- "KGPROD": "NA", \n- "MQ": "60", \n- "NSF": "NA", \n- "NSM": "NA", \n- "NSN": "NA", \n- "PMC": "NA", \n- "POS": "39177761", \n- "QUAL": "1134.77", \n- "REF": "G", \n- "RS": "NA", \n- "SAO": "NA", \n- "TISSUE": "NA", \n- "TUMOR": "NA", \n- "VEST_FDR": "0.15", \n- "VEST_PVALUE": "0.01093"\n- }, \n- {\n- "ALT": "C", \n- "CHASM_FDR": "0.15", \n- "CHASM_PVALUE": "0.093", \n- "CHROM": "chr19", \n- "COSMIC_ID": "COSM3721172", \n- "DP": "12", \n- "GENE": "CCDC9", \n- "KGPROD": "NA", \n- "MQ": "60", \n- "NSF": "NA", \n- "NSM": "NA", \n- "NSN": "NA", \n- "PMC": "NA", \n- "POS": "47271515", \n- "QUAL": "336.77", \n- "REF": "T", \n- "RS": "NA", \n- "SAO": "NA", \n- "TISSUE": "haematopoietic_and_lymphoid_tissue", \n- "TUMOR": "haematopoietic_neoplasm_--_acute_myeloid_leukaemia", \n- "VEST_FDR": "1", \n- "VEST_PVALUE": "0.97622"\n- }, \n- {\n- "ALT": "T", \n- "CHASM_FDR": "0.15", \n- "CHASM_PVALUE": "0.0834", \n- "CHROM": "chr20", \n- "COSMIC_ID": "COSM3758608", \n- "DP": "26", \n- "GENE": "TP53RK", \n- "KGPROD": "NA", \n- "MQ": "60", \n- "NSF": "NA", \n- "NSM": "NA", \n- "NSN": "NA", \n- "PMC": "NA", \n- "POS": "46687147", \n- "QUAL": "423.77", \n- "REF": "C", \n- "RS": "NA", \n- "SAO": "NA", \n- "TISSUE": "pancreas", \n- "TUMOR": "carcinoma_--_ductal_carcinoma", \n- "VEST_FDR": "1", \n- "VEST_PVALUE": "0.88584"\n- }\n- ]\n-}\n\\ No newline at end of file\n' |
| b |
| diff -r c15d9049ab81 -r b591b35283e4 ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/variants.vcf --- a/ctat_mutations-7cf8f5889a4d/test-data/varcalling.outdir/variants.vcf Wed Nov 14 12:20:23 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,79 +0,0 @@\n-##fileformat=VCFv4.2\n-##FILTER=<ID=LowQual,Description="Low quality">\n-##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n-##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n-##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --recover-dangling-heads true --dont-use-soft-clipped-bases true --standard-min-confidence-threshold-for-calling 20.0 --output /broad/hptmp/bankapur/full_mut/varcalling.outdir/variants.vcf --input /broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/recalibrated.bam --reference /seq/regev_genome_portal/RESOURCES/CTAT_GENOME_LIB/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa --emit-ref-confidence NONE --gvcf-gq-bands 1 --gvcf-gq-bands 2 --gvcf-gq-bands 3 --gvcf-gq-bands 4 --gvcf-gq-bands 5 --gvcf-gq-bands 6 --gvcf-gq-bands 7 --gvcf-gq-bands 8 --gvcf-gq-bands 9 --gvcf-gq-bands 10 --gvcf-gq-bands 11 --gvcf-gq-bands 12 --gvcf-gq-bands 13 --gvcf-gq-bands 14 --gvcf-gq-bands 15 --gvcf-gq-bands 16 --gvcf-gq-bands 17 --gvcf-gq-bands 18 --gvcf-gq-bands 19 --gvcf-gq-bands 20 --gvcf-gq-bands 21 --gvcf-gq-bands 22 --gvcf-gq-bands 23 --gvcf-gq-bands 24 --gvcf-gq-bands 25 --gvcf-gq-bands 26 --gvcf-gq-bands 27 --gvcf-gq-bands 28 --gvcf-gq-bands 29 --gvcf-gq-bands 30 --gvcf-gq-bands 31 --gvcf-gq-bands 32 --gvcf-gq-bands 33 --gvcf-gq-bands 34 --gvcf-gq-bands 35 --gvcf-gq-bands 36 --gvcf-gq-bands 37 --gvcf-gq-bands 38 --gvcf-gq-bands 39 --gvcf-gq-bands 40 --gvcf-gq-bands 41 --gvcf-gq-bands 42 --gvcf-gq-bands 43 --gvcf-gq-bands 44 --gvcf-gq-bands 45 --gvcf-gq-bands 46 --gvcf-gq-bands 47 --gvcf-gq-bands 48 --gvcf-gq-bands 49 --gvcf-gq-bands 50 --gvcf-gq-bands 51 --gvcf-gq-bands 52 --gvcf-gq-bands 53 --gvcf-gq-bands 54 --gvcf-gq-bands 55 --gvcf-gq-bands 56 --gvcf-gq-bands 57 --gvcf-gq-bands 58 --gvcf-gq-bands 59 --gvcf-gq-bands 60 --gvcf-gq-bands 70 --gvcf-gq-bands 80 --gvcf-gq-bands 90 --gvcf-gq-bands 99 --indel-size-to-eliminate-in-ref-model 10 --use-alleles-trigger false --disable-optimizations false --just-determine-active-regions false --dont-genotype false --max-mnp-distance 0 --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --do-not-recover-dangling-branches false --min-dangling-branch-length 4 --consensus false --max-num-haplotypes-in-population 128 --error-correct-kmers false --min-pruning 2 --debug-graph-transformations false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --use-new-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotyping-mode DISCOVERY --genotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMI'..b'0.323;SOR=1.525\tGT:AD:DP:GQ:PL\t0/1:38,22:60:99:758,0,1811\n-chr8\t143924022\t.\tA\tG\t587.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=-2.271;DP=58;ExcessHet=3.0103;FS=14.916;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=10.13;ReadPosRankSum=0.674;SOR=2.948\tGT:AD:DP:GQ:PL\t0/1:40,18:58:99:616,0,1892\n-chr12\t56420869\t.\tG\tA\t384.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=2.348;DP=48;ExcessHet=3.0103;FS=4.262;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=8.02;ReadPosRankSum=0.096;SOR=0.674\tGT:AD:DP:GQ:PL\t0/1:30,18:48:99:413,0,759\n-chr12\t56420872\t.\tA\tG\t695.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=-0.308;DP=46;ExcessHet=3.0103;FS=8.803;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=15.13;ReadPosRankSum=0.656;SOR=1.232\tGT:AD:DP:GQ:PL\t0/1:18,28:46:99:724,0,415\n-chr12\t56422138\t.\tC\tT\t72.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=1.718;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=9.10;ReadPosRankSum=-0.816;SOR=0.693\tGT:AD:DP:GQ:PL\t0/1:4,4:8:96:101,0,96\n-chr17\t7673767\t.\tC\tT\t1848.77\t.\tAC=2;AF=1.00;AN=2;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.31;SOR=1.609\tGT:AD:DP:GQ:PL\t1/1:0,61:61:99:1877,183,0\n-chr17\t7675327\t.\tC\tT\t32.74\t.\tAC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=16.37;SOR=0.693\tGT:AD:DP:GQ:PL\t1/1:0,2:2:6:60,6,0\n-chr17\t7676154\t.\tG\tC\t2161.77\t.\tAC=2;AF=1.00;AN=2;BaseQRankSum=3.225;DP=80;ExcessHet=3.0103;FS=14.289;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=27.02;ReadPosRankSum=-2.023;SOR=0.642\tGT:AD:DP:GQ:PL\t1/1:4,76:80:99:2190,183,0\n-chr17\t43071077\t.\tT\tC\t92.03\t.\tAC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=23.01;SOR=3.258\tGT:AD:DP:GQ:PL\t1/1:0,4:4:12:120,12,0\n-chr17\t43082453\t.\tA\tG\t37.74\t.\tAC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=18.87;SOR=2.303\tGT:AD:DP:GQ:PL\t1/1:0,2:2:6:65,6,0\n-chr17\t43091983\t.\tT\tC\t84.03\t.\tAC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=21.01;SOR=0.693\tGT:AD:DP:GQ:PL\t1/1:0,4:4:12:112,12,0\n-chr17\t43092919\t.\tG\tA\t33.74\t.\tAC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=16.87;SOR=2.303\tGT:AD:DP:GQ:PL\t1/1:0,2:2:6:61,6,0\n-chr17\t43093220\t.\tA\tG\t278.77\t.\tAC=2;AF=1.00;AN=2;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.88;SOR=4.804\tGT:AD:DP:GQ:PL\t1/1:0,10:10:30:307,30,0\n-chr17\t43093449\t.\tG\tA\t425.77\t.\tAC=2;AF=1.00;AN=2;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.87;SOR=1.402\tGT:AD:DP:GQ:PL\t1/1:0,9:9:33:454,33,0\n-chr17\t43093454\t.\tC\tT\t425.77\t.\tAC=2;AF=1.00;AN=2;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.78;SOR=1.270\tGT:AD:DP:GQ:PL\t1/1:0,11:11:33:454,33,0\n-chr19\t39177761\t.\tG\tC\t1134.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=2.258;DP=106;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=10.71;ReadPosRankSum=1.397;SOR=0.654\tGT:AD:DP:GQ:PL\t0/1:58,48:106:99:1163,0,1435\n-chr19\t39178960\t.\tA\tATG\t226.77\t.\tAC=2;AF=1.00;AN=2;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.40;SOR=4.174\tGT:AD:DP:GQ:PL\t1/1:0,7:7:21:264,21,0\n-chr19\t39179002\t.\tT\tC\t31.74\t.\tAC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=15.87;SOR=2.303\tGT:AD:DP:GQ:PL\t1/1:0,2:2:6:59,6,0\n-chr19\t47271315\t.\tC\tT\t513.77\t.\tAC=2;AF=1.00;AN=2;BaseQRankSum=0.932;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=25.69;ReadPosRankSum=-1.045;SOR=0.264\tGT:AD:DP:GQ:PL\t1/1:1,19:20:30:542,30,0\n-chr19\t47271515\t.\tT\tC\t336.77\t.\tAC=2;AF=1.00;AN=2;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.06;SOR=2.670\tGT:AD:DP:GQ:PL\t1/1:0,12:12:36:365,36,0\n-chr19\t47272198\t.\tG\tT\t21.77\t.\tAC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=10.88;SOR=0.693\tGT:AD:DP:GQ:PL\t1/1:0,2:2:6:49,6,0\n-chr20\t46687147\t.\tC\tT\t423.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=-0.260;DP=26;ExcessHet=3.0103;FS=1.657;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=16.30;ReadPosRankSum=1.395;SOR=1.179\tGT:AD:DP:GQ:PL\t0/1:8,18:26:99:452,0,165\n' 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| diff -r c15d9049ab81 -r b591b35283e4 ctat_mutations-7cf8f5889a4d/tool-data/cravat_tissues.loc.sample --- a/ctat_mutations-7cf8f5889a4d/tool-data/cravat_tissues.loc.sample Wed Nov 14 12:20:23 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,27 +0,0 @@ -Bladder Bladder Urothelial Carcinoma BLCA (TCGA) Jun 2013 -Blood-Lymphocyte Chronic Lymphocytic Leukemia CLL (ICGC) Mar 2013 -Blood-Myeloid Acute Myeloid Leukemia LAML (TCGA) Jun 2013 -Brain-Cerebellum Medulloblastoma MB (mixed source) Dec 2010 -Brain-Glioblastoma-Multiforme Glioblastoma Multiforme GBM (TCGA) Jun 2013 -Brain-Lower-Grade-Glioma Brain Lower Grade Glioma LGG (TCGA) Jun 2013 -Breast Breast Invasive Carcinoma BRCA (TCGA) Jun 12012 -Cervix Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma CESC (TCGA) Jun 2013 -Colon Colon Adenocarcinoma COAD (TCGA) Jun 2013 -Head and Neck Head and Neck Squamous Cell Carcinoma HNSC (TCGA) Jun 2013 -Kidney-Chromophobe Kidney Chromophobe KICH (TCGA) Jun 2013 -Kidney-Clear-Cell Kidney Renal Clear Cell Carcinoma KIRC (TCGA) Jun 2013 -Kidney-Papillary-Cell Kidney Renal Papillary Cell Carcinoma KIRP (TCGA) Jun 2013 -Liver-Nonviral Hepatocellular Carcinoma (Secondary to Alcohol and Adiposity) HCCA (ICGC) Mar 2013 -Liver-Viral Hepatocellular Carcinoma (Viral) HCCV (ICGC) Mar 2013 -Lung-Adenocarcinoma Lung Adenocarcinoma LUAD (TCGA) Jun 2013 -Lung-Squamous Cell Lung Squamous Cell Carcinoma LUSC (TCGA) Jun 2013 -Melanoma Melanoma ML (Yardena Samuels lab) Dec 2011 -Other General purpose OV (TCGA) Jun 2013 -Ovary Ovarian Serous Cystadenocarcinoma OV (TCGA) Jun 2013 -Pancreas Pancreatic Cancer PNCC (ICGC)) Mar 2013 -Prostate-Adenocarcinoma Prostate Adenocarcinoma PRAD (TCGA) Jun 2013 -Rectum Rectum Adenocarcinoma READ (TCGA) Jun 2013 -Skin Skin Cutaneous Melanoma SKCM (TCGA) Jun 2013 -Stomach Stomach Adenocarcinoma STAD (TCGA) Jun 2013 -Thyroid Thyroid Carcinoma THCA (TCGA) Jun 2013 -Uterus Uterine Corpus Endometriod Carcinoma UCEC (TCGA) Jun 2013 |
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| diff -r c15d9049ab81 -r b591b35283e4 ctat_mutations-7cf8f5889a4d/tool-data/ctat_genome_resource_libs.loc.sample --- a/ctat_mutations-7cf8f5889a4d/tool-data/ctat_genome_resource_libs.loc.sample Wed Nov 14 12:20:23 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,15 +0,0 @@ -# This file lists the locations of CTAT Genome Resource Libraries -# Usually there will only be one library, but it is concievable -# that there could be multiple libraries. -# This file format is as follows -# (white space characters are TAB characters): -# -#<value> <name> <path> -# value is a unique id -# name is the display name -# path is the directory where the genome resource lib files are stored -# -#ctat_genome_resource_libs.loc could look like: -# -#GRCh38_v27_CTAT_lib_Feb092018 CTAT_GenomeResourceLib_GRCh38_v27_CTAT_lib_Feb092018 /path/to/ctat/genome/resource/lib/directory -# |
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| diff -r c15d9049ab81 -r b591b35283e4 ctat_mutations-7cf8f5889a4d/tool_data_table_conf.xml.sample --- a/ctat_mutations-7cf8f5889a4d/tool_data_table_conf.xml.sample Wed Nov 14 12:20:23 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,18 +0,0 @@ -<tables> - <table name="ctat_genome_resource_libs" comment_char="#" allow_duplicate_entries="False"> - <columns>value, name, path</columns> - <file path="tool-data/ctat_genome_resource_libs.loc" /> - </table> - <table name="cravat_tissues" comment_char="#" allow_duplicate_entries="False"> - <columns>value, name, path</columns> - <file path="tool-data/cravat_tissues.loc" /> - </table> - <table name="ctat_centrifuge_indexes" comment_char="#" allow_duplicate_entries="False"> - <columns>value, name, path</columns> - <file path="tool-data/ctat_centrifuge_indexes.loc" /> - </table> - <table name="ctat_lncrna_annotations" comment_char="#" allow_duplicate_entries="False"> - <columns>value, name, path</columns> - <file path="tool-data/ctat_lncrna_annotations.loc" /> - </table> -</tables> |
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| diff -r c15d9049ab81 -r b591b35283e4 ctat_mutations.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_mutations.xml Wed Nov 14 12:34:06 2018 -0500 |
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| @@ -0,0 +1,68 @@ +<tool id="ctat_mutations" name="ctat_mutations" version="1.0.0" profile="17.05"> + <description>Mutation Pipeline for calling SNPs and variants</description> + <requirements> + <requirement type="package" version="2.0.1">ctat-mutations</requirement> + </requirements> + <command detect_errors="default"> + <![CDATA[ + ctat_mutations \ + --plot \ + --out_dir varcalling.outdir \ + --threads 8 \ + --variant_filtering_mode GATK \ + --left "$left" \ + --right "$right" \ + --genome_lib_dir "${genome_resource_lib.fields.path}" \ + --variant_call_mode GATK \ + --tissue_type "$tissue_type" \ + --email "$cravat_email" + ]]> + </command> + <inputs> + <param format="fastq" name="left" type="data" label="Left/Forward strand reads" help="Left read"/> + <param format="fastq" name="right" type="data" label="Right/Reverse strand reads" help="Right read"/> + <param name="tissue_type" type="select" label="Select a pathology" help="If you don't know, just choose 'General Purpose'"> + <options from_data_table="ctat_cravat_tissues"> + <filter type="sort_by" column="1"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> + </options> + </param> + <param name="genome_resource_lib" type="select" label="Select a reference genome"> + <options from_data_table="ctat_genome_resource_libs"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No indexes are available" /> + </options> + </param> + <param name="cravat_email" type="text" label="CRAVAT email" help="CRAVAT registered email id"/> + <section name="adv" title="This service uses the GATK4. GATK4 is licensed by the Broad Institute and is made available to academic users of this service for non-commercial use only. The full text of the license is available here: https://www.broadinstitute.org/gatk/about/license.html. For more information about GATK and full documentation, please visit the GATK website: https://www.broadinstitute.org." expanded="False"> + </section> + </inputs> + <outputs> + <data format="tabular" name="cancertab" label="${tool.name} on ${on_string}: Cancer Tab" from_work_dir="varcalling.outdir/cancer.tab"/> + <data format="vcf" name="cancerVariants" label="${tool.name} on ${on_string}: Cancer VCF" from_work_dir="varcalling.outdir/cancer.vcf"/> + <data format="vcf" name="allVariants" label="${tool.name} on ${on_string}: All Variants VCF" from_work_dir="varcalling.outdir/variants.vcf"/> + <data format="bam" name="bamfile" label="Bam used in haplotype calling" from_work_dir="varcalling.outdir/misc/recalibrated.bam"/> + <data format="txt" name="cravat" label="Annotated (lightly filtered) VCF file" from_work_dir="varcalling.outdir/variants_initial_filtering_clean_snp_RNAedit.vcf_snpeff_updated.vcf.gz"/> + </outputs> + <tests> + <test> + <param name="left" value="reads_1.fastq.gz"/> + <param name="right" value="reads_2.fastq.gz"/> + <param name="tissue_type" value="Other"/> + <output name="cancertab" file="varcalling.outdir/cancer.tab" /> + <output name="cancerVariants" file="varcalling.outdir/cancer.vcf" /> + <output name="allVariants" file="varcalling.outdir/variants.vcf" /> + <output name="bamfile" file="varcalling.outdir/misc/recalibrated.bam" /> + <output name="cravat" file="varcalling.outdir/variants_initial_filtering_clean_snp_RNAedit.vcf_snpeff_updated.vcf.gz"/> + </test> + </tests> + <help> + +.. class:: warningmark + +Mutation detection in RNA-Seq highlights the GATK Best Practices in RNA-Seq variant calling, several sources of variant annotation, and filtering based on CRAVAT. + + </help> + <citations> + </citations> +</tool> |
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| diff -r c15d9049ab81 -r b591b35283e4 test-data/varcalling.outdir/cancer.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/varcalling.outdir/cancer.tab Wed Nov 14 12:34:06 2018 -0500 |
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| @@ -0,0 +1,14 @@ +CHROM POS REF ALT GENE DP QUAL MQ SAO NSF NSM NSN TUMOR TISSUE COSMIC_ID KGPROD RS PMC CHASM_PVALUE CHASM_FDR VEST_PVALUE VEST_FDR +chr5 474989 A G LOC100288152,SLC9A3 4 96.03 60 NA NA NA NA carcinoma_--_NS urinary_tract COSM4006021 NA NA NA 0.1114 0.2 0.96802 1 +chr5 181224474 G A TRIM41 45 349.77 60 NA NA NA NA NA NA NA NA NA NA 0.0694 0.15 0.48052 1 +chr8 143923759 G A PLEC 66 838.77 60 NA NA NA NA carcinoma_--_adenocarcinoma large_intestine COSM3750086 NA NA NA 0.0344 0.1 0.84202 1 +chr12 56420869 G A TIMELESS 48 384.77 60 NA NA NA NA carcinoma_--_adenocarcinoma large_intestine COSM3753397 NA NA NA 0.0744 0.15 0.18439 0.95 +chr17 7673767 C T TP53 61 1848.77 60 NA NA NA NA Ewings_sarcoma-peripheral_primitive_neuroectodermal_tumour_--_NS bone COSM3717625 NA NA NA 0 0.05 0.01447 0.15 +chr17 7676154 G C TP53 80 2161.77 60 NA NA NA NA haematopoietic_neoplasm_--_acute_myeloid_leukaemia haematopoietic_and_lymphoid_tissue COSM3766193 NA NA NA 0.087 0.15 0.52717 1 +chr17 43071077 T C BRCA1 4 92.03 60 NA NA NA NA haematopoietic_neoplasm_--_acute_myeloid_leukaemia haematopoietic_and_lymphoid_tissue COSM3755560 NA NA NA 0.0372 0.1 0.3446 1 +chr17 43091983 T C BRCA1 4 84.03 60 NA NA NA NA haemangioblastoma_--_NS soft_tissue COSM3755561 NA NA NA 0.0002 0.05 0.64447 1 +chr17 43092919 G A BRCA1 2 33.74 60 NA NA NA NA carcinoma_--_NS prostate COSM3755564 NA NA NA 0.0004 0.05 0.33539 1 +chr17 43093454 C T BRCA1 11 425.77 60 NA NA NA NA rhabdomyosarcoma_--_embryonal soft_tissue COSM4989394 NA NA NA 0.0014 0.05 0.51068 1 +chr19 39177761 G C PAK4 106 1134.77 60 NA NA NA NA NA NA NA NA NA NA 0.0004 0.05 0.01093 0.15 +chr19 47271515 T C CCDC9 12 336.77 60 NA NA NA NA haematopoietic_neoplasm_--_acute_myeloid_leukaemia haematopoietic_and_lymphoid_tissue COSM3721172 NA NA NA 0.093 0.15 0.97622 1 +chr20 46687147 C T TP53RK 26 423.77 60 NA NA NA NA carcinoma_--_ductal_carcinoma pancreas COSM3758608 NA NA NA 0.0834 0.15 0.88584 1 |
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| diff -r c15d9049ab81 -r b591b35283e4 test-data/varcalling.outdir/cancer.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/varcalling.outdir/cancer.vcf Wed Nov 14 12:34:06 2018 -0500 |
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| b'@@ -0,0 +1,87 @@\n+##fileformat=VCFv4.2\n+##FILTER=<ID=PASS,Description="All filters passed">\n+##FILTER=<ID=FS,Description="FS > 30.0">\n+##FILTER=<ID=LowQual,Description="Low quality">\n+##FILTER=<ID=QD,Description="QD < 2.0">\n+##FILTER=<ID=SnpCluster,Description="SNPs found in clusters">\n+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n+##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --recover-dangling-heads true --dont-use-soft-clipped-bases true --standard-min-confidence-threshold-for-calling 20.0 --output /broad/hptmp/bankapur/full_mut/varcalling.outdir/variants.vcf --input /broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/recalibrated.bam --reference /seq/regev_genome_portal/RESOURCES/CTAT_GENOME_LIB/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa --emit-ref-confidence NONE --gvcf-gq-bands 1 --gvcf-gq-bands 2 --gvcf-gq-bands 3 --gvcf-gq-bands 4 --gvcf-gq-bands 5 --gvcf-gq-bands 6 --gvcf-gq-bands 7 --gvcf-gq-bands 8 --gvcf-gq-bands 9 --gvcf-gq-bands 10 --gvcf-gq-bands 11 --gvcf-gq-bands 12 --gvcf-gq-bands 13 --gvcf-gq-bands 14 --gvcf-gq-bands 15 --gvcf-gq-bands 16 --gvcf-gq-bands 17 --gvcf-gq-bands 18 --gvcf-gq-bands 19 --gvcf-gq-bands 20 --gvcf-gq-bands 21 --gvcf-gq-bands 22 --gvcf-gq-bands 23 --gvcf-gq-bands 24 --gvcf-gq-bands 25 --gvcf-gq-bands 26 --gvcf-gq-bands 27 --gvcf-gq-bands 28 --gvcf-gq-bands 29 --gvcf-gq-bands 30 --gvcf-gq-bands 31 --gvcf-gq-bands 32 --gvcf-gq-bands 33 --gvcf-gq-bands 34 --gvcf-gq-bands 35 --gvcf-gq-bands 36 --gvcf-gq-bands 37 --gvcf-gq-bands 38 --gvcf-gq-bands 39 --gvcf-gq-bands 40 --gvcf-gq-bands 41 --gvcf-gq-bands 42 --gvcf-gq-bands 43 --gvcf-gq-bands 44 --gvcf-gq-bands 45 --gvcf-gq-bands 46 --gvcf-gq-bands 47 --gvcf-gq-bands 48 --gvcf-gq-bands 49 --gvcf-gq-bands 50 --gvcf-gq-bands 51 --gvcf-gq-bands 52 --gvcf-gq-bands 53 --gvcf-gq-bands 54 --gvcf-gq-bands 55 --gvcf-gq-bands 56 --gvcf-gq-bands 57 --gvcf-gq-bands 58 --gvcf-gq-bands 59 --gvcf-gq-bands 60 --gvcf-gq-bands 70 --gvcf-gq-bands 80 --gvcf-gq-bands 90 --gvcf-gq-bands 99 --indel-size-to-eliminate-in-ref-model 10 --use-alleles-trigger false --disable-optimizations false --just-determine-active-regions false --dont-genotype false --max-mnp-distance 0 --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --do-not-recover-dangling-branches false --min-dangling-branch-length 4 --consensus false --max-num-haplotypes-in-population 128 --error-correct-kmers false --min-pruning 2 --debug-graph-transformations false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --use-new-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --max-alternate-alleles 6 '..b'MLEAF=1;MQ=60;QD=16.87;SOR=2.303;ANN=A|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007300.3|Coding|10/24|c.2612C>T|p.Pro871Leu|2844/7270|2612/5655|871/1884||,A|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007297.3|Coding|9/22|c.2471C>T|p.Pro824Leu|2752/7115|2471/5451|824/1816||,A|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007294.3|Coding|10/23|c.2612C>T|p.Pro871Leu|2844/7207|2612/5592|871/1863||,A|intron_variant|MODIFIER|BRCA1|BRCA1|transcript|NM_007298.3|Coding|9/21|c.787+1825C>T||||||,A|intron_variant|MODIFIER|BRCA1|BRCA1|transcript|NM_007299.3|Coding|10/21|c.787+1825C>T||||||,A|non_coding_exon_variant|MODIFIER|BRCA1|BRCA1|transcript|NR_027676.1|Noncoding|10/23|n.2748C>T||||||;COSMIC_ID=COSM3755564;TISSUE=prostate;TUMOR=carcinoma_--_NS;FATHMM=NEUTRAL;SOMATIC=Confirmed_somatic_variant;CHASM_PVALUE=0.0004;CHASM_FDR=0.05;VEST_PVALUE=0.33539;VEST_FDR=1\tGT:AD:DP:GQ:PL\t1/1:0,2:2:6:61,6,0\n+chr17\t43093454\t.\tC\tT\t425.77\tPASS\tGENE=BRCA1;AC=2;AF=1;AN=2;DP=11;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;QD=31.78;SOR=1.27;ANN=T|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007300.3|Coding|10/24|c.2077G>A|p.Asp693Asn|2309/7270|2077/5655|693/1884||,T|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007297.3|Coding|9/22|c.1936G>A|p.Asp646Asn|2217/7115|1936/5451|646/1816||,T|missense_variant|MODERATE|BRCA1|BRCA1|transcript|NM_007294.3|Coding|10/23|c.2077G>A|p.Asp693Asn|2309/7207|2077/5592|693/1863||,T|intron_variant|MODIFIER|BRCA1|BRCA1|transcript|NM_007298.3|Coding|9/21|c.787+1290G>A||||||,T|intron_variant|MODIFIER|BRCA1|BRCA1|transcript|NM_007299.3|Coding|10/21|c.787+1290G>A||||||,T|non_coding_exon_variant|MODIFIER|BRCA1|BRCA1|transcript|NR_027676.1|Noncoding|10/23|n.2213G>A||||||;COSMIC_ID=COSM4989394;TISSUE=soft_tissue;TUMOR=rhabdomyosarcoma_--_embryonal;FATHMM=NEUTRAL;SOMATIC=Reported_in_another_cancer_sample_as_somatic;CHASM_PVALUE=0.0014;CHASM_FDR=0.05;VEST_PVALUE=0.51068;VEST_FDR=1\tGT:AD:DP:GQ:PL\t1/1:0,11:11:33:454,33,0\n+chr19\t39177761\t.\tG\tC\t1134.77\tPASS\tGENE=PAK4;AC=1;AF=0.5;AN=2;BaseQRankSum=2.258;DP=106;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.5;MQ=60;MQRankSum=0;QD=10.71;ReadPosRankSum=1.397;SOR=0.654;ANN=C|missense_variant|MODERATE|PAK4|PAK4|transcript|NM_001014831.2|Coding|10/11|c.1572G>C|p.Met524Ile|2033/3064|1572/1776|524/591||,C|missense_variant|MODERATE|PAK4|PAK4|transcript|NM_001014832.1|Coding|8/9|c.1572G>C|p.Met524Ile|1734/2765|1572/1776|524/591||,C|missense_variant|MODERATE|PAK4|PAK4|transcript|NM_001014834.2|Coding|7/8|c.1113G>C|p.Met371Ile|1275/2306|1113/1317|371/438||,C|missense_variant|MODERATE|PAK4|PAK4|transcript|NM_001014835.1|Coding|8/9|c.1113G>C|p.Met371Ile|1348/2379|1113/1317|371/438||,C|missense_variant|MODERATE|PAK4|PAK4|transcript|NM_005884.3|Coding|9/10|c.1572G>C|p.Met524Ile|1807/2838|1572/1776|524/591||;CHASM_PVALUE=0.0004;CHASM_FDR=0.05;VEST_PVALUE=0.01093;VEST_FDR=0.15\tGT:AD:DP:GQ:PL\t0/1:58,48:106:99:1163,0,1435\n+chr19\t47271515\t.\tT\tC\t336.77\tPASS\tGENE=CCDC9;AC=2;AF=1;AN=2;DP=12;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;QD=28.06;SOR=2.67;ANN=C|missense_variant|MODERATE|CCDC9|CCDC9|transcript|NM_015603.2|Coding|12/12|c.1433T>C|p.Leu478Pro|1640/2078|1433/1596|478/531||;COSMIC_ID=COSM3721172;TISSUE=haematopoietic_and_lymphoid_tissue;TUMOR=haematopoietic_neoplasm_--_acute_myeloid_leukaemia;FATHMM=NEUTRAL;SOMATIC=Confirmed_somatic_variant;CHASM_PVALUE=0.093;CHASM_FDR=0.15;VEST_PVALUE=0.97622;VEST_FDR=1\tGT:AD:DP:GQ:PL\t1/1:0,12:12:36:365,36,0\n+chr20\t46687147\t.\tC\tT\t423.77\tPASS\tGENE=TP53RK;AC=1;AF=0.5;AN=2;BaseQRankSum=-0.26;DP=26;ExcessHet=3.0103;FS=1.657;MLEAC=1;MLEAF=0.5;MQ=60;MQRankSum=0;QD=16.3;ReadPosRankSum=1.395;SOR=1.179;ANN=T|missense_variant|MODERATE|TP53RK|TP53RK|transcript|NM_033550.3|Coding|2/2|c.368G>A|p.Arg123Gln|591/3373|368/762|123/253||;COSMIC_ID=COSM3758608;TISSUE=pancreas;TUMOR=carcinoma_--_ductal_carcinoma;FATHMM=PATHOGENIC;SOMATIC=Confirmed_somatic_variant;CHASM_PVALUE=0.0834;CHASM_FDR=0.15;VEST_PVALUE=0.88584;VEST_FDR=1\tGT:AD:DP:GQ:PL\t0/1:8,18:26:99:452,0,165\n' |
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| diff -r c15d9049ab81 -r b591b35283e4 test-data/varcalling.outdir/misc/recalibrated.bai |
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| Binary file test-data/varcalling.outdir/misc/recalibrated.bai has changed |
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| diff -r c15d9049ab81 -r b591b35283e4 test-data/varcalling.outdir/misc/recalibrated.bam |
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| Binary file test-data/varcalling.outdir/misc/recalibrated.bam has changed |
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| diff -r c15d9049ab81 -r b591b35283e4 test-data/varcalling.outdir/mutation_inspector.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/varcalling.outdir/mutation_inspector.json Wed Nov 14 12:34:06 2018 -0500 |
| [ |
| b'@@ -0,0 +1,321 @@\n+{\n+ "BAM": "/broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/recalibrated.bam", \n+ "BAM_INDEX": "/broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/recalibrated.bai", \n+ "BED": "/seq/regev_genome_portal/RESOURCES/CTAT_GENOME_LIB/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ctat_mutation_lib/refGene.sort.bed", \n+ "BED_INDEX": "/seq/regev_genome_portal/RESOURCES/CTAT_GENOME_LIB/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ctat_mutation_lib/refGene.sort.bed.idx", \n+ "SAMPLE": "varcalling.outdir", \n+ "SNV": [\n+ {\n+ "ALT": "G", \n+ "CHASM_FDR": "0.2", \n+ "CHASM_PVALUE": "0.1114", \n+ "CHROM": "chr5", \n+ "COSMIC_ID": "COSM4006021", \n+ "DP": "4", \n+ "GENE": "LOC100288152,SLC9A3", \n+ "KGPROD": "NA", \n+ "MQ": "60", \n+ "NSF": "NA", \n+ "NSM": "NA", \n+ "NSN": "NA", \n+ "PMC": "NA", \n+ "POS": "474989", \n+ "QUAL": "96.03", \n+ "REF": "A", \n+ "RS": "NA", \n+ "SAO": "NA", \n+ "TISSUE": "urinary_tract", \n+ "TUMOR": "carcinoma_--_NS", \n+ "VEST_FDR": "1", \n+ "VEST_PVALUE": "0.96802"\n+ }, \n+ {\n+ "ALT": "A", \n+ "CHASM_FDR": "0.15", \n+ "CHASM_PVALUE": "0.0694", \n+ "CHROM": "chr5", \n+ "COSMIC_ID": "NA", \n+ "DP": "45", \n+ "GENE": "TRIM41", \n+ "KGPROD": "NA", \n+ "MQ": "60", \n+ "NSF": "NA", \n+ "NSM": "NA", \n+ "NSN": "NA", \n+ "PMC": "NA", \n+ "POS": "181224474", \n+ "QUAL": "349.77", \n+ "REF": "G", \n+ "RS": "NA", \n+ "SAO": "NA", \n+ "TISSUE": "NA", \n+ "TUMOR": "NA", \n+ "VEST_FDR": "1", \n+ "VEST_PVALUE": "0.48052"\n+ }, \n+ {\n+ "ALT": "A", \n+ "CHASM_FDR": "0.1", \n+ "CHASM_PVALUE": "0.0344", \n+ "CHROM": "chr8", \n+ "COSMIC_ID": "COSM3750086", \n+ "DP": "66", \n+ "GENE": "PLEC", \n+ "KGPROD": "NA", \n+ "MQ": "60", \n+ "NSF": "NA", \n+ "NSM": "NA", \n+ "NSN": "NA", \n+ "PMC": "NA", \n+ "POS": "143923759", \n+ "QUAL": "838.77", \n+ "REF": "G", \n+ "RS": "NA", \n+ "SAO": "NA", \n+ "TISSUE": "large_intestine", \n+ "TUMOR": "carcinoma_--_adenocarcinoma", \n+ "VEST_FDR": "1", \n+ "VEST_PVALUE": "0.84202"\n+ }, \n+ {\n+ "ALT": "A", \n+ "CHASM_FDR": "0.15", \n+ "CHASM_PVALUE": "0.0744", \n+ "CHROM": "chr12", \n+ "COSMIC_ID": "COSM3753397", \n+ "DP": "48", \n+ "GENE": "TIMELESS", \n+ "KGPROD": "NA", \n+ "MQ": "60", \n+ "NSF": "NA", \n+ "NSM": "NA", \n+ "NSN": "NA", \n+ "PMC": "NA", \n+ "POS": "56420869", \n+ "QUAL": "384.77", \n+ "REF": "G", \n+ "RS": "NA", \n+ "SAO": "NA", \n+ "TISSUE": "large_intestine", \n+ "TUMOR": "carcinoma_--_adenocarcinoma", \n+ "VEST_FDR": "0.95", \n+ "VEST_PVALUE": "0.18439"\n+ }, \n+ {\n+ "ALT": "T", \n+ "CHASM_FDR": "0.05", \n+ "CHASM_PVALUE": "0", \n+ "CHROM": "chr17", \n+ "COSMIC_ID": "COSM3717625", \n+ "DP": "61", \n+ "GENE": "TP53", \n+ "KGPROD": "NA", \n+ "MQ": "60", \n+ "NSF": "NA", \n+ "NSM": "NA", \n+ "NSN": "NA", \n+ "PMC": "NA", \n+ "POS": "7673767", \n+ "QUAL": "1848.77", \n+ "REF": "C", \n+ "RS": "NA", \n+ "SAO": "NA", \n+ "TISSUE": "bone", \n+ "TUMOR": "Ewings_sarcoma-peripheral_primitive_neuroectodermal_tumour_--_NS", \n+ "VEST_FDR": "0.15", \n+ "VEST_PVALUE": "0.01447"\n+ }, \n+ {\n+ "ALT": "C", \n+ "CHASM_FDR": "0.15", \n+ "CHASM_PVALUE": "0.087", \n+ "CHROM": "chr17", \n+ "COSMIC_ID": "COSM3766193", \n+ "DP": "80", \n+ "GENE": "TP53", \n+ "KGPROD": "NA", \n+ "MQ": "60", \n+ "NSF": "NA", \n+ "NSM": "NA", \n+ "NSN": "NA", \n+ "PMC": "NA", \n+ "POS": "7676154", \n+ "QUAL": "2161.77", \n+ "REF": "G", \n+ "RS": "NA", \n+ "SAO": "NA", \n+ "TISSUE": "haematopoietic_and_lymphoid_tissue", \n+ "TUMOR":'..b'"4", \n+ "GENE": "BRCA1", \n+ "KGPROD": "NA", \n+ "MQ": "60", \n+ "NSF": "NA", \n+ "NSM": "NA", \n+ "NSN": "NA", \n+ "PMC": "NA", \n+ "POS": "43071077", \n+ "QUAL": "92.03", \n+ "REF": "T", \n+ "RS": "NA", \n+ "SAO": "NA", \n+ "TISSUE": "haematopoietic_and_lymphoid_tissue", \n+ "TUMOR": "haematopoietic_neoplasm_--_acute_myeloid_leukaemia", \n+ "VEST_FDR": "1", \n+ "VEST_PVALUE": "0.3446"\n+ }, \n+ {\n+ "ALT": "C", \n+ "CHASM_FDR": "0.05", \n+ "CHASM_PVALUE": "0.0002", \n+ "CHROM": "chr17", \n+ "COSMIC_ID": "COSM3755561", \n+ "DP": "4", \n+ "GENE": "BRCA1", \n+ "KGPROD": "NA", \n+ "MQ": "60", \n+ "NSF": "NA", \n+ "NSM": "NA", \n+ "NSN": "NA", \n+ "PMC": "NA", \n+ "POS": "43091983", \n+ "QUAL": "84.03", \n+ "REF": "T", \n+ "RS": "NA", \n+ "SAO": "NA", \n+ "TISSUE": "soft_tissue", \n+ "TUMOR": "haemangioblastoma_--_NS", \n+ "VEST_FDR": "1", \n+ "VEST_PVALUE": "0.64447"\n+ }, \n+ {\n+ "ALT": "A", \n+ "CHASM_FDR": "0.05", \n+ "CHASM_PVALUE": "0.0004", \n+ "CHROM": "chr17", \n+ "COSMIC_ID": "COSM3755564", \n+ "DP": "2", \n+ "GENE": "BRCA1", \n+ "KGPROD": "NA", \n+ "MQ": "60", \n+ "NSF": "NA", \n+ "NSM": "NA", \n+ "NSN": "NA", \n+ "PMC": "NA", \n+ "POS": "43092919", \n+ "QUAL": "33.74", \n+ "REF": "G", \n+ "RS": "NA", \n+ "SAO": "NA", \n+ "TISSUE": "prostate", \n+ "TUMOR": "carcinoma_--_NS", \n+ "VEST_FDR": "1", \n+ "VEST_PVALUE": "0.33539"\n+ }, \n+ {\n+ "ALT": "T", \n+ "CHASM_FDR": "0.05", \n+ "CHASM_PVALUE": "0.0014", \n+ "CHROM": "chr17", \n+ "COSMIC_ID": "COSM4989394", \n+ "DP": "11", \n+ "GENE": "BRCA1", \n+ "KGPROD": "NA", \n+ "MQ": "60", \n+ "NSF": "NA", \n+ "NSM": "NA", \n+ "NSN": "NA", \n+ "PMC": "NA", \n+ "POS": "43093454", \n+ "QUAL": "425.77", \n+ "REF": "C", \n+ "RS": "NA", \n+ "SAO": "NA", \n+ "TISSUE": "soft_tissue", \n+ "TUMOR": "rhabdomyosarcoma_--_embryonal", \n+ "VEST_FDR": "1", \n+ "VEST_PVALUE": "0.51068"\n+ }, \n+ {\n+ "ALT": "C", \n+ "CHASM_FDR": "0.05", \n+ "CHASM_PVALUE": "0.0004", \n+ "CHROM": "chr19", \n+ "COSMIC_ID": "NA", \n+ "DP": "106", \n+ "GENE": "PAK4", \n+ "KGPROD": "NA", \n+ "MQ": "60", \n+ "NSF": "NA", \n+ "NSM": "NA", \n+ "NSN": "NA", \n+ "PMC": "NA", \n+ "POS": "39177761", \n+ "QUAL": "1134.77", \n+ "REF": "G", \n+ "RS": "NA", \n+ "SAO": "NA", \n+ "TISSUE": "NA", \n+ "TUMOR": "NA", \n+ "VEST_FDR": "0.15", \n+ "VEST_PVALUE": "0.01093"\n+ }, \n+ {\n+ "ALT": "C", \n+ "CHASM_FDR": "0.15", \n+ "CHASM_PVALUE": "0.093", \n+ "CHROM": "chr19", \n+ "COSMIC_ID": "COSM3721172", \n+ "DP": "12", \n+ "GENE": "CCDC9", \n+ "KGPROD": "NA", \n+ "MQ": "60", \n+ "NSF": "NA", \n+ "NSM": "NA", \n+ "NSN": "NA", \n+ "PMC": "NA", \n+ "POS": "47271515", \n+ "QUAL": "336.77", \n+ "REF": "T", \n+ "RS": "NA", \n+ "SAO": "NA", \n+ "TISSUE": "haematopoietic_and_lymphoid_tissue", \n+ "TUMOR": "haematopoietic_neoplasm_--_acute_myeloid_leukaemia", \n+ "VEST_FDR": "1", \n+ "VEST_PVALUE": "0.97622"\n+ }, \n+ {\n+ "ALT": "T", \n+ "CHASM_FDR": "0.15", \n+ "CHASM_PVALUE": "0.0834", \n+ "CHROM": "chr20", \n+ "COSMIC_ID": "COSM3758608", \n+ "DP": "26", \n+ "GENE": "TP53RK", \n+ "KGPROD": "NA", \n+ "MQ": "60", \n+ "NSF": "NA", \n+ "NSM": "NA", \n+ "NSN": "NA", \n+ "PMC": "NA", \n+ "POS": "46687147", \n+ "QUAL": "423.77", \n+ "REF": "C", \n+ "RS": "NA", \n+ "SAO": "NA", \n+ "TISSUE": "pancreas", \n+ "TUMOR": "carcinoma_--_ductal_carcinoma", \n+ "VEST_FDR": "1", \n+ "VEST_PVALUE": "0.88584"\n+ }\n+ ]\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r c15d9049ab81 -r b591b35283e4 test-data/varcalling.outdir/variants.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/varcalling.outdir/variants.vcf Wed Nov 14 12:34:06 2018 -0500 |
| b |
| b'@@ -0,0 +1,79 @@\n+##fileformat=VCFv4.2\n+##FILTER=<ID=LowQual,Description="Low quality">\n+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n+##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --recover-dangling-heads true --dont-use-soft-clipped-bases true --standard-min-confidence-threshold-for-calling 20.0 --output /broad/hptmp/bankapur/full_mut/varcalling.outdir/variants.vcf --input /broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/recalibrated.bam --reference /seq/regev_genome_portal/RESOURCES/CTAT_GENOME_LIB/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa --emit-ref-confidence NONE --gvcf-gq-bands 1 --gvcf-gq-bands 2 --gvcf-gq-bands 3 --gvcf-gq-bands 4 --gvcf-gq-bands 5 --gvcf-gq-bands 6 --gvcf-gq-bands 7 --gvcf-gq-bands 8 --gvcf-gq-bands 9 --gvcf-gq-bands 10 --gvcf-gq-bands 11 --gvcf-gq-bands 12 --gvcf-gq-bands 13 --gvcf-gq-bands 14 --gvcf-gq-bands 15 --gvcf-gq-bands 16 --gvcf-gq-bands 17 --gvcf-gq-bands 18 --gvcf-gq-bands 19 --gvcf-gq-bands 20 --gvcf-gq-bands 21 --gvcf-gq-bands 22 --gvcf-gq-bands 23 --gvcf-gq-bands 24 --gvcf-gq-bands 25 --gvcf-gq-bands 26 --gvcf-gq-bands 27 --gvcf-gq-bands 28 --gvcf-gq-bands 29 --gvcf-gq-bands 30 --gvcf-gq-bands 31 --gvcf-gq-bands 32 --gvcf-gq-bands 33 --gvcf-gq-bands 34 --gvcf-gq-bands 35 --gvcf-gq-bands 36 --gvcf-gq-bands 37 --gvcf-gq-bands 38 --gvcf-gq-bands 39 --gvcf-gq-bands 40 --gvcf-gq-bands 41 --gvcf-gq-bands 42 --gvcf-gq-bands 43 --gvcf-gq-bands 44 --gvcf-gq-bands 45 --gvcf-gq-bands 46 --gvcf-gq-bands 47 --gvcf-gq-bands 48 --gvcf-gq-bands 49 --gvcf-gq-bands 50 --gvcf-gq-bands 51 --gvcf-gq-bands 52 --gvcf-gq-bands 53 --gvcf-gq-bands 54 --gvcf-gq-bands 55 --gvcf-gq-bands 56 --gvcf-gq-bands 57 --gvcf-gq-bands 58 --gvcf-gq-bands 59 --gvcf-gq-bands 60 --gvcf-gq-bands 70 --gvcf-gq-bands 80 --gvcf-gq-bands 90 --gvcf-gq-bands 99 --indel-size-to-eliminate-in-ref-model 10 --use-alleles-trigger false --disable-optimizations false --just-determine-active-regions false --dont-genotype false --max-mnp-distance 0 --dont-trim-active-regions false --max-disc-ar-extension 25 --max-gga-ar-extension 300 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --do-not-recover-dangling-branches false --min-dangling-branch-length 4 --consensus false --max-num-haplotypes-in-population 128 --error-correct-kmers false --min-pruning 2 --debug-graph-transformations false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --debug false --use-filtered-reads-for-annotations false --bam-writer-type CALLED_HAPLOTYPES --capture-assembly-failure-bam false --error-correct-reads false --do-not-run-physical-phasing false --min-base-quality-score 10 --smith-waterman JAVA --use-new-qual-calculator false --annotate-with-num-discovered-alleles false --heterozygosity 0.001 --indel-heterozygosity 1.25E-4 --heterozygosity-stdev 0.01 --max-alternate-alleles 6 --max-genotype-count 1024 --sample-ploidy 2 --num-reference-samples-if-no-call 0 --genotyping-mode DISCOVERY --genotype-filtered-alleles false --contamination-fraction-to-filter 0.0 --output-mode EMI'..b'0.323;SOR=1.525\tGT:AD:DP:GQ:PL\t0/1:38,22:60:99:758,0,1811\n+chr8\t143924022\t.\tA\tG\t587.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=-2.271;DP=58;ExcessHet=3.0103;FS=14.916;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=10.13;ReadPosRankSum=0.674;SOR=2.948\tGT:AD:DP:GQ:PL\t0/1:40,18:58:99:616,0,1892\n+chr12\t56420869\t.\tG\tA\t384.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=2.348;DP=48;ExcessHet=3.0103;FS=4.262;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=8.02;ReadPosRankSum=0.096;SOR=0.674\tGT:AD:DP:GQ:PL\t0/1:30,18:48:99:413,0,759\n+chr12\t56420872\t.\tA\tG\t695.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=-0.308;DP=46;ExcessHet=3.0103;FS=8.803;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=15.13;ReadPosRankSum=0.656;SOR=1.232\tGT:AD:DP:GQ:PL\t0/1:18,28:46:99:724,0,415\n+chr12\t56422138\t.\tC\tT\t72.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=1.718;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=9.10;ReadPosRankSum=-0.816;SOR=0.693\tGT:AD:DP:GQ:PL\t0/1:4,4:8:96:101,0,96\n+chr17\t7673767\t.\tC\tT\t1848.77\t.\tAC=2;AF=1.00;AN=2;DP=61;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=30.31;SOR=1.609\tGT:AD:DP:GQ:PL\t1/1:0,61:61:99:1877,183,0\n+chr17\t7675327\t.\tC\tT\t32.74\t.\tAC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=16.37;SOR=0.693\tGT:AD:DP:GQ:PL\t1/1:0,2:2:6:60,6,0\n+chr17\t7676154\t.\tG\tC\t2161.77\t.\tAC=2;AF=1.00;AN=2;BaseQRankSum=3.225;DP=80;ExcessHet=3.0103;FS=14.289;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=27.02;ReadPosRankSum=-2.023;SOR=0.642\tGT:AD:DP:GQ:PL\t1/1:4,76:80:99:2190,183,0\n+chr17\t43071077\t.\tT\tC\t92.03\t.\tAC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=23.01;SOR=3.258\tGT:AD:DP:GQ:PL\t1/1:0,4:4:12:120,12,0\n+chr17\t43082453\t.\tA\tG\t37.74\t.\tAC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=18.87;SOR=2.303\tGT:AD:DP:GQ:PL\t1/1:0,2:2:6:65,6,0\n+chr17\t43091983\t.\tT\tC\t84.03\t.\tAC=2;AF=1.00;AN=2;DP=4;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=21.01;SOR=0.693\tGT:AD:DP:GQ:PL\t1/1:0,4:4:12:112,12,0\n+chr17\t43092919\t.\tG\tA\t33.74\t.\tAC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=16.87;SOR=2.303\tGT:AD:DP:GQ:PL\t1/1:0,2:2:6:61,6,0\n+chr17\t43093220\t.\tA\tG\t278.77\t.\tAC=2;AF=1.00;AN=2;DP=10;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.88;SOR=4.804\tGT:AD:DP:GQ:PL\t1/1:0,10:10:30:307,30,0\n+chr17\t43093449\t.\tG\tA\t425.77\t.\tAC=2;AF=1.00;AN=2;DP=9;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.87;SOR=1.402\tGT:AD:DP:GQ:PL\t1/1:0,9:9:33:454,33,0\n+chr17\t43093454\t.\tC\tT\t425.77\t.\tAC=2;AF=1.00;AN=2;DP=11;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=31.78;SOR=1.270\tGT:AD:DP:GQ:PL\t1/1:0,11:11:33:454,33,0\n+chr19\t39177761\t.\tG\tC\t1134.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=2.258;DP=106;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=10.71;ReadPosRankSum=1.397;SOR=0.654\tGT:AD:DP:GQ:PL\t0/1:58,48:106:99:1163,0,1435\n+chr19\t39178960\t.\tA\tATG\t226.77\t.\tAC=2;AF=1.00;AN=2;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=32.40;SOR=4.174\tGT:AD:DP:GQ:PL\t1/1:0,7:7:21:264,21,0\n+chr19\t39179002\t.\tT\tC\t31.74\t.\tAC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=15.87;SOR=2.303\tGT:AD:DP:GQ:PL\t1/1:0,2:2:6:59,6,0\n+chr19\t47271315\t.\tC\tT\t513.77\t.\tAC=2;AF=1.00;AN=2;BaseQRankSum=0.932;DP=21;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQRankSum=0.000;QD=25.69;ReadPosRankSum=-1.045;SOR=0.264\tGT:AD:DP:GQ:PL\t1/1:1,19:20:30:542,30,0\n+chr19\t47271515\t.\tT\tC\t336.77\t.\tAC=2;AF=1.00;AN=2;DP=12;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=28.06;SOR=2.670\tGT:AD:DP:GQ:PL\t1/1:0,12:12:36:365,36,0\n+chr19\t47272198\t.\tG\tT\t21.77\t.\tAC=2;AF=1.00;AN=2;DP=2;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=10.88;SOR=0.693\tGT:AD:DP:GQ:PL\t1/1:0,2:2:6:49,6,0\n+chr20\t46687147\t.\tC\tT\t423.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=-0.260;DP=26;ExcessHet=3.0103;FS=1.657;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=16.30;ReadPosRankSum=1.395;SOR=1.179\tGT:AD:DP:GQ:PL\t0/1:8,18:26:99:452,0,165\n' 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| diff -r c15d9049ab81 -r b591b35283e4 test-data/varcalling.outdir/variants.vcf.idx |
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| Binary file test-data/varcalling.outdir/variants.vcf.idx has changed |
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| diff -r c15d9049ab81 -r b591b35283e4 test-data/varcalling.outdir/variants_initial_filtering_clean_snp_RNAedit.vcf_snpeff_updated.vcf.gz |
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| Binary file test-data/varcalling.outdir/variants_initial_filtering_clean_snp_RNAedit.vcf_snpeff_updated.vcf.gz has changed |
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| diff -r c15d9049ab81 -r b591b35283e4 tool-data/cravat_tissues.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/cravat_tissues.loc.sample Wed Nov 14 12:34:06 2018 -0500 |
| b |
| @@ -0,0 +1,27 @@ +Bladder Bladder Urothelial Carcinoma BLCA (TCGA) Jun 2013 +Blood-Lymphocyte Chronic Lymphocytic Leukemia CLL (ICGC) Mar 2013 +Blood-Myeloid Acute Myeloid Leukemia LAML (TCGA) Jun 2013 +Brain-Cerebellum Medulloblastoma MB (mixed source) Dec 2010 +Brain-Glioblastoma-Multiforme Glioblastoma Multiforme GBM (TCGA) Jun 2013 +Brain-Lower-Grade-Glioma Brain Lower Grade Glioma LGG (TCGA) Jun 2013 +Breast Breast Invasive Carcinoma BRCA (TCGA) Jun 12012 +Cervix Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma CESC (TCGA) Jun 2013 +Colon Colon Adenocarcinoma COAD (TCGA) Jun 2013 +Head and Neck Head and Neck Squamous Cell Carcinoma HNSC (TCGA) Jun 2013 +Kidney-Chromophobe Kidney Chromophobe KICH (TCGA) Jun 2013 +Kidney-Clear-Cell Kidney Renal Clear Cell Carcinoma KIRC (TCGA) Jun 2013 +Kidney-Papillary-Cell Kidney Renal Papillary Cell Carcinoma KIRP (TCGA) Jun 2013 +Liver-Nonviral Hepatocellular Carcinoma (Secondary to Alcohol and Adiposity) HCCA (ICGC) Mar 2013 +Liver-Viral Hepatocellular Carcinoma (Viral) HCCV (ICGC) Mar 2013 +Lung-Adenocarcinoma Lung Adenocarcinoma LUAD (TCGA) Jun 2013 +Lung-Squamous Cell Lung Squamous Cell Carcinoma LUSC (TCGA) Jun 2013 +Melanoma Melanoma ML (Yardena Samuels lab) Dec 2011 +Other General purpose OV (TCGA) Jun 2013 +Ovary Ovarian Serous Cystadenocarcinoma OV (TCGA) Jun 2013 +Pancreas Pancreatic Cancer PNCC (ICGC)) Mar 2013 +Prostate-Adenocarcinoma Prostate Adenocarcinoma PRAD (TCGA) Jun 2013 +Rectum Rectum Adenocarcinoma READ (TCGA) Jun 2013 +Skin Skin Cutaneous Melanoma SKCM (TCGA) Jun 2013 +Stomach Stomach Adenocarcinoma STAD (TCGA) Jun 2013 +Thyroid Thyroid Carcinoma THCA (TCGA) Jun 2013 +Uterus Uterine Corpus Endometriod Carcinoma UCEC (TCGA) Jun 2013 |
| b |
| diff -r c15d9049ab81 -r b591b35283e4 tool-data/ctat_genome_resource_libs.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/ctat_genome_resource_libs.loc.sample Wed Nov 14 12:34:06 2018 -0500 |
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| @@ -0,0 +1,15 @@ +# This file lists the locations of CTAT Genome Resource Libraries +# Usually there will only be one library, but it is concievable +# that there could be multiple libraries. +# This file format is as follows +# (white space characters are TAB characters): +# +#<value> <name> <path> +# value is a unique id +# name is the display name +# path is the directory where the genome resource lib files are stored +# +#ctat_genome_resource_libs.loc could look like: +# +#GRCh38_v27_CTAT_lib_Feb092018 CTAT_GenomeResourceLib_GRCh38_v27_CTAT_lib_Feb092018 /path/to/ctat/genome/resource/lib/directory +# |
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| diff -r c15d9049ab81 -r b591b35283e4 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Nov 14 12:34:06 2018 -0500 |
| b |
| @@ -0,0 +1,18 @@ +<tables> + <table name="ctat_genome_resource_libs" comment_char="#" allow_duplicate_entries="False"> + <columns>value, name, path</columns> + <file path="tool-data/ctat_genome_resource_libs.loc" /> + </table> + <table name="cravat_tissues" comment_char="#" allow_duplicate_entries="False"> + <columns>value, name, path</columns> + <file path="tool-data/cravat_tissues.loc" /> + </table> + <table name="ctat_centrifuge_indexes" comment_char="#" allow_duplicate_entries="False"> + <columns>value, name, path</columns> + <file path="tool-data/ctat_centrifuge_indexes.loc" /> + </table> + <table name="ctat_lncrna_annotations" comment_char="#" allow_duplicate_entries="False"> + <columns>value, name, path</columns> + <file path="tool-data/ctat_lncrna_annotations.loc" /> + </table> +</tables> |