Mercurial > repos > iuc > vardict_java
changeset 1:5f756651a1bc draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 2690164244722cfc32811015f2408b8275f06378"
| author | iuc |
|---|---|
| date | Fri, 11 Sep 2020 21:07:13 +0000 |
| parents | 2975b29bcaa1 |
| children | d262577e04b0 |
| files | macros.xml test-data/all_variants_paired.vcf test-data/all_variants_single.vcf test-data/passed_variants_paired.vcf test-data/passed_variants_single.vcf vardict.xml |
| diffstat | 6 files changed, 72 insertions(+), 62 deletions(-) [+] |
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--- a/macros.xml Tue Aug 25 05:41:19 2020 -0400 +++ b/macros.xml Fri Sep 11 21:07:13 2020 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@VERSION_SUFFIX@">0</token> - <token name="@TOOL_VERSION@">1.7.0</token> + <token name="@TOOL_VERSION@">1.8.1</token> <xml name="ref_select"> <conditional name="reference_source"> <param name="reference_source_selector" type="select" label="Choose the source for the reference genome file"> @@ -17,6 +17,11 @@ </when> </conditional> </xml> + <xml name="stdio"> + <stdio> + <regex match="java.lang.OutOfMemoryError" source="stderr" level="fatal_oom" description="Out of memory error occurred" /> + </stdio> + </xml> <xml name="input_default"> <param name="tumor" type="data" format="bam" label="Tumor file" /> <param name="interval_file" type="data" format="txt" optional="true" label="Chromosomes" help="Restrict SNV calls to the following list of chromosomes (one per line)" />
--- a/test-data/all_variants_paired.vcf Tue Aug 25 05:41:19 2020 -0400 +++ b/test-data/all_variants_paired.vcf Fri Sep 11 21:07:13 2020 +0000 @@ -1,10 +1,11 @@ -##fileformat=VCFv4.1 +##fileformat=VCFv4.3 +##source=VarDict_v1.8.1 ##INFO=<ID=SAMPLE,Number=1,Type=String,Description="Sample name (with whitespace translated to underscores)"> ##INFO=<ID=TYPE,Number=1,Type=String,Description="Variant Type: SNV Insertion Deletion Complex"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> ##INFO=<ID=END,Number=1,Type=Integer,Description="Chr End Position"> ##INFO=<ID=VD,Number=1,Type=Integer,Description="Variant Depth"> -##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> +##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency"> ##INFO=<ID=SHIFT3,Number=1,Type=Integer,Description="No. of bases to be shifted to 3 prime for deletions due to alternative alignment"> ##INFO=<ID=MSI,Number=1,Type=Float,Description="MicroSatellite. > 1 indicates MSI"> ##INFO=<ID=MSILEN,Number=1,Type=Float,Description="MSI unit repeat length in bp"> @@ -13,6 +14,8 @@ ##INFO=<ID=LSEQ,Number=1,Type=String,Description="5' flanking seq"> ##INFO=<ID=RSEQ,Number=1,Type=String,Description="3' flanking seq"> ##INFO=<ID=STATUS,Number=1,Type=String,Description="Somatic or germline status"> +##INFO=<ID=P0.01Likely,Number=0,Type=Flag,Description="Likely candidate but p-value > 0.01/5**vd2 (means the evidence in tumor sample might be weak, e.g. small diff in AF)"> +##INFO=<ID=InDelLikely,Number=0,Type=Flag,Description="Likely indels more than 2bp are not considered somatic (weak evidence of presence in normal samples)"> ##FILTER=<ID=q22.5,Description="Mean Base Quality Below 22.5"> ##FILTER=<ID=Q0,Description="Mean Mapping Quality Below 0"> ##FILTER=<ID=p8,Description="Mean Position in Reads Less than 8"> @@ -25,8 +28,6 @@ ##FILTER=<ID=f0.01,Description="Allele frequency < 0.01"> ##FILTER=<ID=P0.05,Description="Not significant with p-value > 0.05"> ##FILTER=<ID=DIFF0.2,Description="Non-somatic or LOH and allele frequency difference < 0.2"> -##FILTER=<ID=P0.01Likely,Description="Likely candidate but p-value > 0.01/5**vd2"> -##FILTER=<ID=InDelLikely,Description="Likely Indels are not considered somatic"> ##FILTER=<ID=MSI12,Description="Variant in MSI region with 12 non-monomer MSI or 12 monomer MSI"> ##FILTER=<ID=NM5.25,Description="Mean mismatches in reads >= 5.25, thus likely false positive"> ##FILTER=<ID=InGap,Description="The somatic variant is in the deletion gap, thus likely false positive"> @@ -39,67 +40,67 @@ ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> ##FORMAT=<ID=ALD,Number=2,Type=Integer,Description="Variant forward, reverse reads"> ##FORMAT=<ID=RD,Number=2,Type=Integer,Description="Reference forward, reverse reads"> -##FORMAT=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> +##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele Frequency"> ##FORMAT=<ID=ADJAF,Number=1,Type=Float,Description="Adjusted AF for indels due to local realignment"> -##FORMAT=<ID=BIAS,Number=1,Type=String,Description="Strand Bias Info"> +##FORMAT=<ID=BIAS,Number=2,Type=String,Description="Strand Bias Info"> ##FORMAT=<ID=PMEAN,Number=1,Type=Float,Description="Mean position in reads"> ##FORMAT=<ID=PSTD,Number=1,Type=Float,Description="Position STD in reads"> ##FORMAT=<ID=QUAL,Number=1,Type=Float,Description="Mean quality score in reads"> ##FORMAT=<ID=QSTD,Number=1,Type=Float,Description="Quality score STD in reads"> ##FORMAT=<ID=SBF,Number=1,Type=Float,Description="Strand Bias Fisher p-value"> ##FORMAT=<ID=ODDRATIO,Number=1,Type=Float,Description="Strand Bias Odds ratio"> -##FORMAT=<ID=MQ,Number=1,Type=Float,Description="Mean Mapping Quality"> +##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="Mean Mapping Quality"> ##FORMAT=<ID=SN,Number=1,Type=Float,Description="Signal to noise"> ##FORMAT=<ID=HIAF,Number=1,Type=Float,Description="Allele frequency using only high quality bases"> ##FORMAT=<ID=NM,Number=1,Type=Float,Description="Mean mismatches in reads"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Tumor Normal chrM 150 . T C 121 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTTTGATTCCTGCCTCAT;RSEQ=CTATTATTTATCGCACCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:35:1:40.5:1:1:0:60:4:1:0:1.5 1/1:9:9:4,5:0,0:0,9:1:0,2:29.8:1:38.4:1:1:0:60:18:1:0.1111:1.8 chrM 195 . C T 120 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=1;VD=1;AF=1;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATATTACAGGCGAACATAC;RSEQ=TACTAAAGTGTGTTAATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:22:0:40:0:1:0:60:2:1:0:2 1/1:9:9:3,6:0,0:0,9:1:0,2:21.9:1:37.9:1:1:0:60:18:1:0:1.8 -chrM 295 . C T 75 d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5 STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACATCATAACAAAAAATTT;RSEQ=CACCAAACCCCCCCCTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:4,0:0,0:0,4:1:0,0:19.5:1:37.5:1:1:0:60:8:1:0:2.2 -chrM 302 . AC A 85 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=Deletion;DP=0;VD=0;AF=0;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAACAAAAAATTTCCACCAA;RSEQ=CCCCCCCTCCCCCCGCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:5:5,0:1,0:1,5:0.8333:0,0:15.2:1:36.8:1:1:0:60:10:0.8333:0.5:1.6 +chrM 295 . C T 75 d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5 STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACATCATAACAAAAAATTT;RSEQ=CACCAAACCCCCCCCTCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0 1/1:4:4:4,0:0,0:0,4:1:0,0:19.5:1:37.5:1:1:0:60:8:1:0:2.2 +chrM 302 . AC A 85 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=Deletion;DP=0;VD=0;AF=0;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAACAAAAAATTTCCACCAA;RSEQ=CCCCCCCTCCCCCCGCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:5:5,0:1,0:1,5:0.8333:0,0:15.2:1:36.8:1:1:0:60:10:0.8333:0.5:1.6 chrM 410 . A T 149 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATTTCAAATTTTATCTTT;RSEQ=GGCGGTATGCACTTTTAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:23.3:1:36.7:1:1:0:60:6:1:0.3333:2.3 1/1:18:18:12,6:0,0:0,18:1:0,2:19.7:1:35.9:1:1:0:60:17:1:0.0556:1.9 -chrM 464 . C T 193 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=8;VD=8;AF=1;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.85965;SOR=Inf;LSEQ=TAACACATTATTTTCCCCTC;RSEQ=CACTCCCATACTACTAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:6,2:0,0:0,8:1:0,2:22.8:1:36.2:1:1:0:60:16:1:0:2.1 1/1:49:48:37,11:1,0:1,48:0.9796:0,2:24.9:1:34.6:1:1:0:60:15:0.9783:0.0408:2.2 -chrM 491 . T C 228 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=10;VD=10;AF=1;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.89474;SOR=Inf;LSEQ=CATACTACTAATCTCATCAA;RSEQ=ACAACCCCCGCCCATCCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:8,2:0,0:0,10:1:0,2:28.3:1:38.3:1:1:0:60:20:1:0:1.7 1/1:85:84:65,19:1,0:1,84:0.9882:0,2:21:1:35.7:1:1:0:60:27:0.9878:0.0824:1.7 -chrM 681 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=Tumor;TYPE=SNV;DP=124;VD=2;AF=0.0161;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02084;SOR=Inf;LSEQ=TCCTAGCCTTTCTATTAGCT;RSEQ=TTAGTAAGATTACACATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:70,52:122,2:0.0161:2,2:36:1:30.5:1:1:1.34287:49:4:0.0163:0:1 0/0:732:0:0,0:418,314:732,0:0:2,0:25:1:37.4:1:1:0:54.8:60:1:0:0.1 -chrM 692 . T C 38 v3 STATUS=StrongSomatic;SAMPLE=Tumor;TYPE=SNV;DP=124;VD=2;AF=0.0161;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02079;SOR=Inf;LSEQ=CTATTAGCTCTTAGTAAGAT;RSEQ=ACACATGCAAGCATCCCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:73,49:122,2:0.0161:2,2:36:1:38:1:1:1.48485:49:4:0.0163:0:1 0/0:733:0:0,0:419,314:733,0:0:2,0:24.6:1:37.1:1:1:0:54.9:121.167:1:0:0.1 -chrM 737 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=Tumor;TYPE=SNV;DP=106;VD=2;AF=0.0189;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02224;SOR=Inf;LSEQ=GTGAGTTCACCCTCTAAATC;RSEQ=CCACGATCAAAAGGGACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:42,61:103,2:0.0189:2,2:14.5:1:30.5:1:1:1.45:60:4:0.0202:0.0094:1 0/0:602:0:0,0:228,374:602,0:0:2,0:27.9:1:34.8:1:1:0:59.2:15.27:1:0:0.1 +chrM 464 . C T 193 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=8;VD=8;AF=1;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.85965;SOR=0;LSEQ=TAACACATTATTTTCCCCTC;RSEQ=CACTCCCATACTACTAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:6,2:0,0:0,8:1:0,2:22.8:1:36.2:1:1:0:60:16:1:0:2.1 1/1:49:48:37,11:1,0:1,48:0.9796:0,2:24.9:1:34.6:1:1:0:60:15:0.9783:0.0408:2.2 +chrM 491 . T C 228 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=10;VD=10;AF=1;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.89474;SOR=0;LSEQ=CATACTACTAATCTCATCAA;RSEQ=ACAACCCCCGCCCATCCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:8,2:0,0:0,10:1:0,2:28.3:1:38.3:1:1:0:60:20:1:0:1.7 1/1:85:84:65,19:1,0:1,84:0.9882:0,2:21:1:35.7:1:1:0:60:27:0.9878:0.0824:1.7 +chrM 681 . C T 30 v3 STATUS=StrongSomatic;SAMPLE=Tumor;TYPE=SNV;DP=124;VD=2;AF=0.0161;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.02084;SOR=0;LSEQ=TCCTAGCCTTTCTATTAGCT;RSEQ=TTAGTAAGATTACACATGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:70,52:122,2:0.0161:2,2:36:1:30.5:1:1:1.34287:49:4:0.0163:0:1 0/0:732:0:0,0:418,314:732,0:0:2,0:25:1:37.4:1:1:0:55:60:1:0:0.1 +chrM 692 . T C 38 v3 STATUS=StrongSomatic;SAMPLE=Tumor;TYPE=SNV;DP=124;VD=2;AF=0.0161;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.02079;SOR=0;LSEQ=CTATTAGCTCTTAGTAAGAT;RSEQ=ACACATGCAAGCATCCCCGT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:124:2:1,1:73,49:122,2:0.0161:2,2:36:1:38:1:1:1.48485:49:4:0.0163:0:1 0/0:733:0:0,0:419,314:733,0:0:2,0:24.6:1:37.1:1:1:0:55:121.167:1:0:0.1 +chrM 737 . A G 30 v3 STATUS=StrongSomatic;SAMPLE=Tumor;TYPE=SNV;DP=106;VD=2;AF=0.0189;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.02224;SOR=0;LSEQ=GTGAGTTCACCCTCTAAATC;RSEQ=CCACGATCAAAAGGGACAAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:106:2:1,1:42,61:103,2:0.0189:2,2:14.5:1:30.5:1:1:1.45:60:4:0.0202:0.0094:1 0/0:602:0:0,0:228,374:602,0:0:2,0:27.9:1:34.8:1:1:0:59:15.27:1:0:0.1 chrM 1735 . C T 140 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCTTAGCCAAACCATTTAC;RSEQ=CAAATAAAGTATAGGCGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:46.7:1:40.3:1:1:0:60:6:1:0:1 1/1:14:14:6,8:0,0:0,14:1:0,2:26:1:37:1:1:0:60:28:1:0:1.1 chrM 2354 . C T 135 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCATAAGCCTGCGTCAGAT;RSEQ=AAAACACTGAACTGACAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:18.3:1:36.5:1:1:0:60:6:1:0.3333:1 1/1:11:11:8,3:0,0:0,11:1:0,2:23.1:1:39.1:1:1:0:60:22:1:0.0909:1.3 chrM 2395 . C A 35 d5;v3;f0.01 STATUS=StrongLOH;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=0;AF=0;SHIFT3=2;MSI=2.000;MSILEN=1;SSF=0.62857;SOR=0;LSEQ=AACAGCCCAATATCTACAAT;RSEQ=AACCAACAAGTCATTATTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:1,2:3,0:0:2,0:22.3:1:36.7:1:1:0:60:6:1:0:1 0/1:12:2:1,1:5,5:10,2:0.1667:2,2:42:1:35:1:1:1:60:4:0.1667:0:1.5 -chrM 2485 . C T 123 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTAAAAGGAACTCGGCAAA;RSEQ=CTTACCCCGCCTGTTTACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:17.7:1:37.7:1:1:0:53.3:6:1:0:1 1/1:13:13:8,5:0,0:0,13:1:0,2:29.4:1:33.5:1:1:0:40.2:5.5:1:0:1.2 +chrM 2485 . C T 123 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTAAAAGGAACTCGGCAAA;RSEQ=CTTACCCCGCCTGTTTACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:17.7:1:37.7:1:1:0:53:6:1:0:1 1/1:13:13:8,5:0,0:0,13:1:0,2:29.4:1:33.5:1:1:0:40:5.5:1:0:1.2 chrM 2493 . C T 32 d5;v3;f0.01 STATUS=StrongLOH;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.81429;SOR=0;LSEQ=GAACTCGGCAAACCTTACCC;RSEQ=GCCTGTTTACCAAAAACATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:2,0:2,0:0:0,0:24:1:37:1:1:0:50:4:1:0:1 0/1:19:2:1,1:10,7:17,2:0.1053:2,2:42:1:32.5:1:1:1.40151:13:4:0.1053:0:2 -chrM 3012 . G A 99 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTTGGATCAGGACATCCC;RSEQ=ATGGTGCAGCCGCTATTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:1,5:0,0:0,6:1:0,2:36.7:1:38.5:1:1:0:58.2:12:1:0:1.2 -chrM 3394 . C T 35 d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5 STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCGAACGAAAAATTCTAGG;RSEQ=TATATACAACTACGCAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 0/1:14:2:1,1:7,5:12,2:0.1429:2,2:25.5:1:35.5:1:1:1.36624:60:4:0.1429:0:1 +chrM 3012 . G A 99 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTTGGATCAGGACATCCC;RSEQ=ATGGTGCAGCCGCTATTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:1,5:0,0:0,6:1:0,2:36.7:1:38.5:1:1:0:58:12:1:0:1.2 +chrM 3394 . C T 35 d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5 STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCGAACGAAAAATTCTAGG;RSEQ=TATATACAACTACGCAAAGG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0 0/1:14:2:1,1:7,5:12,2:0.1429:2,2:25.5:1:35.5:1:1:1.36624:60:4:0.1429:0:1 chrM 3588 . C A 32 d5;v3;f0.01 STATUS=StrongLOH;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=0;AF=0;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=0.62857;SOR=0;LSEQ=CCCCCTCCCCATACCCAACC;RSEQ=CCTGGTCAACCTCAACCTAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:15.7:1:39.7:1:1:0:60:6:1:0:0 0/1:12:2:1,1:5,5:10,2:0.1667:2,2:28:1:32.5:1:1:1:60:4:0.1667:0:1 -chrM 5581 . C T 133 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGCAATACTTAATTTCTG;RSEQ=AACAGCTAAGGACTGCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:12:12:2,10:0,0:0,12:1:0,2:24.8:1:37.3:1:1:0:33.6:24:1:0.0833:1 -chrM 6720 . T C 75 d5 STATUS=SampleSpecific;SAMPLE=Tumor;TYPE=SNV;DP=4;VD=4;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACCATTTGGATACATAGG;RSEQ=ATGGTCTGAGCTATGATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:25:1:37.5:1:1:0:56:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 +chrM 5581 . C T 133 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGCAATACTTAATTTCTG;RSEQ=AACAGCTAAGGACTGCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0 1/1:12:12:2,10:0,0:0,12:1:0,2:24.8:1:37.3:1:1:0:34:24:1:0.0833:1 +chrM 6720 . T C 75 d5 STATUS=SampleSpecific;SAMPLE=Tumor;TYPE=SNV;DP=4;VD=4;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GAACCATTTGGATACATAGG;RSEQ=ATGGTCTGAGCTATGATATC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:25:1:37.5:1:1:0:56:8:1:0:1 0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0 chrM 7877 . C T 34 d5;v3;f0.01 STATUS=StrongLOH;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=0;AF=0;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=0.85979;SOR=0;LSEQ=AACGATCCCTCCCTTACCAT;RSEQ=AAATCAATTGGCCACCAATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:2:0:0,0:1,1:2,0:0:2,0:18:1:37.5:1:1:0:60:4:1:0:0 0/1:26:2:1,1:12,12:24,2:0.0769:2,2:24.5:1:34:1:1:1:60:4:0.0769:0:1 -chrM 8270 . G A 54 d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5 STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCCCGTATTTACCCTATA;RSEQ=CACCCCCTCTACCCCCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:12.7:1:34.3:1:1:0:60:6:1:0:1 +chrM 8270 . G A 54 d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5 STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GGGCCCGTATTTACCCTATA;RSEQ=CACCCCCTCTACCCCCTCTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:12.7:1:34.3:1:1:0:60:6:1:0:1 chrM 8702 . G A 126 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAACCTCAAAACAAATGATA;RSEQ=CCATACACAACACTAAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:46:1:34:1:1:0:60:4:1:0:1.5 1/1:11:11:6,5:0,0:0,11:1:0,2:25.2:1:36.7:1:1:0:51:22:1:0:1 -chrM 9378 . G A 110 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACTAACCATATACCAATG;RSEQ=TGGCGCGATGTAACACGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:20.3:1:36:1:1:0:46:6:1:0:1 1/1:9:9:4,5:0,0:0,9:1:0,2:19.7:1:34.9:1:1:0:44.3:8:1:0.1111:1.2 +chrM 9378 . G A 110 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACTAACCATATACCAATG;RSEQ=TGGCGCGATGTAACACGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:20.3:1:36:1:1:0:46:6:1:0:1 1/1:9:9:4,5:0,0:0,9:1:0,2:19.7:1:34.9:1:1:0:44:8:1:0.1111:1.2 chrM 9541 . C T 58 d5;v3 STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCTAGCCCCTACCCCCCAA;RSEQ=TAGGAGGGCACTGGCCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:48.5:1:37:1:1:0:60:4:1:0:1 1/1:3:3:2,1:0,0:0,3:1:0,2:22.3:1:37:1:1:0:60:6:1:0:1 chrM 10874 . C T 37 d5;v3 STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=5.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTAATTATTAGCATCATCCC;RSEQ=CTACTATTTTTTAACCAAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:30:1:37.5:1:1:0:60:4:1:0:1 1/1:2:2:1,1:0,0:0,2:1:0,2:19:1:37.8:1:1:0:60:4:1:0.5:1 -chrM 11018 . C T 84 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCAACGCCACTTATCCAG;RSEQ=GAACCACTATCACGAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:2,3:0,0:0,5:1:0,2:29.6:1:36.4:1:1:0:51.2:10:1:0:1.2 -chrM 11198 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=Tumor;TYPE=SNV;DP=9;VD=2;AF=0.2222;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12;SOR=Inf;LSEQ=CCAGAACGCCTGAACGCAGG;RSEQ=ACATACTTCCTATTCTACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:31.5:1:31.5:1:1:1.29:60:4:0.2222:0:1.5 0/0:16:0:0,0:10,6:16,0:0:2,0:26.3:1:37.2:1:1:0:60:32:1:0:0.5 +chrM 11018 . C T 84 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCAACGCCACTTATCCAG;RSEQ=GAACCACTATCACGAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:2,3:0,0:0,5:1:0,2:29.6:1:36.4:1:1:0:51:10:1:0:1.2 +chrM 11198 . C A 31 v3 STATUS=StrongSomatic;SAMPLE=Tumor;TYPE=SNV;DP=9;VD=2;AF=0.2222;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=0.12;SOR=0;LSEQ=CCAGAACGCCTGAACGCAGG;RSEQ=ACATACTTCCTATTCTACAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:9:2:1,1:3,4:7,2:0.2222:2,2:31.5:1:31.5:1:1:1.29:60:4:0.2222:0:1.5 0/0:16:0:0,0:10,6:16,0:0:2,0:26.3:1:37.2:1:1:0:60:32:1:0:0.5 chrM 11252 . A G 150 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=5;VD=5;AF=1;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCCCCTACTCATCGCACT;RSEQ=ATTTACACTCACAACACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:0,5:1:0,2:26.2:1:37.4:1:1:0:60:10:1:0.2:1.2 1/1:17:17:9,8:0,0:0,17:1:0,2:27.8:1:36.9:1:1:0:60:34:1:0.0588:1.2 -chrM 11464 . T A 32 PASS STATUS=StrongSomatic;SAMPLE=Tumor;TYPE=SNV;DP=6;VD=2;AF=0.3333;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.125;SOR=Inf;LSEQ=AATAGTACTTGCCGCAGTAC;RSEQ=CTTAAAACTAGGCGGCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:25.5:1:32:1:1:1:60:4:0.3333:0:1 0/0:10:0:0,0:6,4:10,0:0:2,0:24.9:1:37:1:1:0:60:20:1:0:0.2 +chrM 11464 . T A 32 PASS STATUS=StrongSomatic;SAMPLE=Tumor;TYPE=SNV;DP=6;VD=2;AF=0.3333;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.125;SOR=0;LSEQ=AATAGTACTTGCCGCAGTAC;RSEQ=CTTAAAACTAGGCGGCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:25.5:1:32:1:1:1:60:4:0.3333:0:1 0/0:10:0:0,0:6,4:10,0:0:2,0:24.9:1:37:1:1:0:60:20:1:0:0.2 chrM 11492 . A G 33 v3;f0.01 STATUS=StrongLOH;SAMPLE=Tumor;TYPE=SNV;DP=6;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.40441;SOR=0;LSEQ=CTAGGCGGCTATGGTATAAT;RSEQ=CGCCTCACACTCATTCTCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:6:0:0,0:3,3:6,0:0:2,0:33.8:1:33.5:1:1:0:60:12:1:0:0.3 0/1:11:2:1,1:5,4:9,2:0.1818:2,2:23:1:33:1:1:1.22474:60:4:0.1818:0.0909:1 -chrM 11723 . C T 144 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCATAATCGCCCACGGACT;RSEQ=ACATCCTCATTACTATTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:16:16:8,8:0,0:0,16:1:0,2:30.1:1:36.2:1:1:0:50.4:32:1:0:1 -chrM 12613 . A G 106 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATAATATTCATCCCTGT;RSEQ=GCATTGTTCGTTACATGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:7:7:2,5:0,0:0,7:1:0,2:17.9:1:37.9:1:1:0:60:14:1:0:1.3 +chrM 11723 . C T 144 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCATAATCGCCCACGGACT;RSEQ=ACATCCTCATTACTATTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0 1/1:16:16:8,8:0,0:0,16:1:0,2:30.1:1:36.2:1:1:0:50:32:1:0:1 +chrM 12613 . A G 106 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATAATATTCATCCCTGT;RSEQ=GCATTGTTCGTTACATGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0 1/1:7:7:2,5:0,0:0,7:1:0,2:17.9:1:37.9:1:1:0:60:14:1:0:1.3 chrM 12706 . T C 97 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=1;VD=1;AF=1;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTCAAATATCTACTCAT;RSEQ=TTCCTAATTACCATACTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:39:0:40:0:1:0:60:2:1:0:1 1/1:6:6:4,2:0,0:0,6:1:0,2:28.7:1:37.7:1:1:0:60:12:1:0:1.3 chrM 12851 . G A 141 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=4;VD=4;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACAGCAGCCATTCAAGCA;RSEQ=TCCTATACAACCGTATCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:22.5:1:36.5:1:1:0:60:8:1:0:1 1/1:14:14:7,7:0,0:0,14:1:0,2:26.2:1:37.2:1:1:0:60:28:1:0:1.1 chrM 13591 . G A 37 d5;v3;f0.01 STATUS=StrongLOH;SAMPLE=Tumor;TYPE=SNV;DP=4;VD=0;AF=0;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.63158;SOR=0;LSEQ=ACTCTCATCGCTACCTCCCT;RSEQ=ACAAGCGCCTATAGCACTCG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:4:0:0,0:2,2:4,0:0:2,0:17.2:1:34.5:1:1:0:60:8:1:0:0 0/1:16:2:1,1:7,7:14,2:0.125:2,2:17.5:1:37.5:1:1:1:60:4:0.125:0:2 chrM 13618 . T C 38 d5;v3;f0.01 STATUS=StrongLOH;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=0;AF=0;SHIFT3=0;MSI=2.000;MSILEN=3;SSF=0.66912;SOR=0;LSEQ=GCCTATAGCACTCGAATAAT;RSEQ=CTTCTCACCCTAACAGGTCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:3:0:0,0:2,1:3,0:0:2,0:16:1:35.3:1:1:0:60:6:1:0:0.3 0/1:14:2:1,1:4,8:12,2:0.1429:2,2:44.5:1:38.5:1:1:1.90:60:4:0.1429:0:2 chrM 13709 . G A 103 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAACCCCATTAAACGCCTG;RSEQ=CAGCCGGAAGCCTATTCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:32:1:1:0:60:4:1:0:1 1/1:7:7:3,4:0,0:0,7:1:0,2:22.3:1:36.7:1:1:0:60:14:1:0:1 -chrM 14213 . C T 130 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAATGTTCAACCAGTAAC;RSEQ=ACTACTAATCAACGCCCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:11:11:5,6:0,0:0,11:1:0,2:25.2:1:37.7:1:1:0:58.1:22:1:0:1.2 -chrM 14581 . G A 141 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=5;VD=5;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCACACCGCTAACAATCA;RSEQ=TACTAAACCCCCATAAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1:0,2:24.8:1:37.4:1:1:0:43.6:10:1:0:1 1/1:15:15:9,6:0,0:0,15:1:0,2:31.5:1:36.1:1:1:0:56.3:14:1:0.0667:1 -chrM 14794 . A G 37 PASS STATUS=StrongSomatic;SAMPLE=Tumor;TYPE=SNV;DP=6;VD=2;AF=0.3333;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06494;SOR=Inf;LSEQ=CCTAATAAAATTAATTAACC;RSEQ=CTCATTCATCGACCTCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:23:1:37:1:1:1:60:4:0.3333:0.1667:1 0/0:16:0:0,0:6,10:16,0:0:2,0:22.6:1:30.3:1:1:0:60:15:1:0:0 +chrM 14213 . C T 130 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAATGTTCAACCAGTAAC;RSEQ=ACTACTAATCAACGCCCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0 1/1:11:11:5,6:0,0:0,11:1:0,2:25.2:1:37.7:1:1:0:58:22:1:0:1.2 +chrM 14581 . G A 141 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=5;VD=5;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCACACCGCTAACAATCA;RSEQ=TACTAAACCCCCATAAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1:0,2:24.8:1:37.4:1:1:0:44:10:1:0:1 1/1:15:15:9,6:0,0:0,15:1:0,2:31.5:1:36.1:1:1:0:56:14:1:0.0667:1 +chrM 14794 . A G 37 PASS STATUS=StrongSomatic;SAMPLE=Tumor;TYPE=SNV;DP=6;VD=2;AF=0.3333;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06494;SOR=0;LSEQ=CCTAATAAAATTAATTAACC;RSEQ=CTCATTCATCGACCTCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:23:1:37:1:1:1:60:4:0.3333:0.1667:1 0/0:16:0:0,0:6,10:16,0:0:2,0:22.6:1:30.3:1:1:0:60:15:1:0:0 chrM 14906 . A G 177 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=9;VD=9;AF=1;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACAGGACTATTCCTAGCCAT;RSEQ=CACTACTCACCAGACGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:5,4:0,0:0,9:1:0,2:28.8:1:34.1:1:1:0:60:8:1:0.1111:2.1 1/1:33:33:15,18:0,0:0,33:1:0,2:22.5:1:35.2:1:1:0:60:66:1:0.0606:1.8 -chrM 14928 . A G 181 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=9;VD=9;AF=1;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.8;SOR=Inf;LSEQ=ACTACTCACCAGACGCCTCA;RSEQ=CCGCCTTTTCATCAATCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:5,4:0,0:0,9:1:0,2:30:1:38.8:1:1:0:60:18:1:0:2.1 1/1:36:35:16,19:0,1:1,35:0.9722:0,2:20.1:1:35.3:1:1:0:60:16.5:0.9706:0.0833:1.8 +chrM 14928 . A G 181 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=9;VD=9;AF=1;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.8;SOR=0;LSEQ=ACTACTCACCAGACGCCTCA;RSEQ=CCGCCTTTTCATCAATCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:5,4:0,0:0,9:1:0,2:30:1:38.8:1:1:0:60:18:1:0:2.1 1/1:36:35:16,19:0,1:1,35:0.9722:0,2:20.1:1:35.3:1:1:0:60:16.5:0.9706:0.0833:1.8 chrM 15302 . A G 128 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTACCTTTCACTTCATCTT;RSEQ=CCCTTCATTATTGCAGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:38:1:1:0:60:4:1:0:1 1/1:11:11:4,7:0,0:0,11:1:0,2:31.2:1:37.1:1:1:0:60:22:1:0:1.2 -chrM 15453 . C A 83 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTCGGCTTACTTCTCTTC;RSEQ=TTCTCTCCTTAATGACATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:3,3:0,0:0,6:1:0,2:22.7:1:32.2:1:1:0:60:12:1:0:1 -chrM 15933 . C T 57 d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5 STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGTCTTGTAAACCGGAGA;RSEQ=GAAAACCTTTTTCCAAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:11.7:1:36:1:1:0:60:6:1:0:1 -chrM 16070 . C T 107 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACCACCCAAGTATTGACT;RSEQ=ACCCATCAACAACCGCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:7:7:4,3:0,0:0,7:1:0,2:27.4:1:38.4:1:1:0:60:14:1:0:1.7 +chrM 15453 . C A 83 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTCGGCTTACTTCTCTTC;RSEQ=TTCTCTCCTTAATGACATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:3,3:0,0:0,6:1:0,2:22.7:1:32.2:1:1:0:60:12:1:0:1 +chrM 15933 . C T 57 d5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5 STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCAGTCTTGTAAACCGGAGA;RSEQ=GAAAACCTTTTTCCAAGGAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0 1/1:3:3:1,2:0,0:0,3:1:0,2:11.7:1:36:1:1:0:60:6:1:0:1 +chrM 16070 . C T 107 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACCACCCAAGTATTGACT;RSEQ=ACCCATCAACAACCGCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0 1/1:7:7:4,3:0,0:0,7:1:0,2:27.4:1:38.4:1:1:0:60:14:1:0:1.7 chrM 16127 . T C 85 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=1;VD=1;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCAGCCACCATGAATATTG;RSEQ=ACGGTACCATAAATACTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:15:0:41:0:1:0:60:2:1:0:5 1/1:5:5:4,1:0,0:0,5:1:0,2:24.2:1:36.7:1:1:0:60:10:1:0.4:4.2 chrM 16146 . G A 106 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=1;VD=1;AF=1;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACGGTACCATAAATACTT;RSEQ=ACCACCTGTAGTACATAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:34:0:41:0:1:0:60:2:1:0:5 1/1:8:8:6,2:0,0:0,8:1:0,2:15.6:1:35.4:1:1:0:60:7:1:0.25:4.9 chrM 16173 . C T 120 d5;v3;NM5.25 STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TGTAGTACATAAAAACCCAA;RSEQ=CCACATCAAACCCCCCCCCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:37.5:1:1:0:60:4:1:0:5.5 1/1:10:10:6,4:0,0:0,10:1:0,2:26.6:1:36.2:1:1:0:60:20:1:0:5.4 @@ -108,4 +109,4 @@ chrM 16224 . CT TC 159 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=Complex;DP=2;VD=1;AF=0.5;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24901;SOR=0.12566;LSEQ=AAGCAAGTACAGCAATCAAC;RSEQ=TCAACTATCACACATCAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,0:0,1:0.5:0,0:42:0:38:0:1:0:60:2:0.5:0:5 1/1:21:19:9,10:0,0:0,19:0.9048:0,2:26.4:1:37.6:1:1:0:60:38:1:0.0952:3.2 chrM 16263 . C T 158 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=4;VD=4;AF=1;SHIFT3=4;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGCAACTCCAAAGCCACC;RSEQ=CTCACCCACTAGGATACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:25.8:1:34.2:1:1:0:60:3:1:0:3 1/1:18:18:9,9:0,0:0,18:1:0,2:26.9:1:38:1:1:0:60:36:1:0.0556:2.5 chrM 16322 . T C 125 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGTACATAGTACATAAAG;RSEQ=CATTTACCGTACATAGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:13.5:1:33.2:1:1:0:60:4:1:0.5:1.5 1/1:10:10:4,6:0,0:0,10:1:0,2:23.6:1:37.8:1:1:0:60:20:1:0:1.5 -chrM 16521 . C T 113 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGGTTCCTACTTCAGGG;RSEQ=CATAAAGCCTAAATAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:38:1:1:0:51.5:4:1:0:1 1/1:11:11:5,6:0,0:0,11:1:0,2:20.8:1:32.9:1:1:0:49.6:2.667:1:0.0909:1 +chrM 16521 . C T 113 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGGTTCCTACTTCAGGG;RSEQ=CATAAAGCCTAAATAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:38:1:1:0:52:4:1:0:1 1/1:11:11:5,6:0,0:0,11:1:0,2:20.8:1:32.9:1:1:0:50:2.667:1:0.0909:1
--- a/test-data/all_variants_single.vcf Tue Aug 25 05:41:19 2020 -0400 +++ b/test-data/all_variants_single.vcf Fri Sep 11 21:07:13 2020 +0000 @@ -1,4 +1,5 @@ -##fileformat=VCFv4.1 +##fileformat=VCFv4.3 +##source=VarDict_v1.8.1 ##INFO=<ID=SAMPLE,Number=1,Type=String,Description="Sample name (with whitespace translated to underscores)"> ##INFO=<ID=TYPE,Number=1,Type=String,Description="Variant Type: SNV Insertion Deletion Complex"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
--- a/test-data/passed_variants_paired.vcf Tue Aug 25 05:41:19 2020 -0400 +++ b/test-data/passed_variants_paired.vcf Fri Sep 11 21:07:13 2020 +0000 @@ -1,10 +1,11 @@ -##fileformat=VCFv4.1 +##fileformat=VCFv4.3 +##source=VarDict_v1.8.1 ##INFO=<ID=SAMPLE,Number=1,Type=String,Description="Sample name (with whitespace translated to underscores)"> ##INFO=<ID=TYPE,Number=1,Type=String,Description="Variant Type: SNV Insertion Deletion Complex"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> ##INFO=<ID=END,Number=1,Type=Integer,Description="Chr End Position"> ##INFO=<ID=VD,Number=1,Type=Integer,Description="Variant Depth"> -##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> +##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency"> ##INFO=<ID=SHIFT3,Number=1,Type=Integer,Description="No. of bases to be shifted to 3 prime for deletions due to alternative alignment"> ##INFO=<ID=MSI,Number=1,Type=Float,Description="MicroSatellite. > 1 indicates MSI"> ##INFO=<ID=MSILEN,Number=1,Type=Float,Description="MSI unit repeat length in bp"> @@ -13,6 +14,8 @@ ##INFO=<ID=LSEQ,Number=1,Type=String,Description="5' flanking seq"> ##INFO=<ID=RSEQ,Number=1,Type=String,Description="3' flanking seq"> ##INFO=<ID=STATUS,Number=1,Type=String,Description="Somatic or germline status"> +##INFO=<ID=P0.01Likely,Number=0,Type=Flag,Description="Likely candidate but p-value > 0.01/5**vd2 (means the evidence in tumor sample might be weak, e.g. small diff in AF)"> +##INFO=<ID=InDelLikely,Number=0,Type=Flag,Description="Likely indels more than 2bp are not considered somatic (weak evidence of presence in normal samples)"> ##FILTER=<ID=q22.5,Description="Mean Base Quality Below 22.5"> ##FILTER=<ID=Q0,Description="Mean Mapping Quality Below 0"> ##FILTER=<ID=p8,Description="Mean Position in Reads Less than 8"> @@ -25,8 +28,6 @@ ##FILTER=<ID=f0.01,Description="Allele frequency < 0.01"> ##FILTER=<ID=P0.05,Description="Not significant with p-value > 0.05"> ##FILTER=<ID=DIFF0.2,Description="Non-somatic or LOH and allele frequency difference < 0.2"> -##FILTER=<ID=P0.01Likely,Description="Likely candidate but p-value > 0.01/5**vd2"> -##FILTER=<ID=InDelLikely,Description="Likely Indels are not considered somatic"> ##FILTER=<ID=MSI12,Description="Variant in MSI region with 12 non-monomer MSI or 12 monomer MSI"> ##FILTER=<ID=NM5.25,Description="Mean mismatches in reads >= 5.25, thus likely false positive"> ##FILTER=<ID=InGap,Description="The somatic variant is in the deletion gap, thus likely false positive"> @@ -39,49 +40,49 @@ ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> ##FORMAT=<ID=ALD,Number=2,Type=Integer,Description="Variant forward, reverse reads"> ##FORMAT=<ID=RD,Number=2,Type=Integer,Description="Reference forward, reverse reads"> -##FORMAT=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> +##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele Frequency"> ##FORMAT=<ID=ADJAF,Number=1,Type=Float,Description="Adjusted AF for indels due to local realignment"> -##FORMAT=<ID=BIAS,Number=1,Type=String,Description="Strand Bias Info"> +##FORMAT=<ID=BIAS,Number=2,Type=String,Description="Strand Bias Info"> ##FORMAT=<ID=PMEAN,Number=1,Type=Float,Description="Mean position in reads"> ##FORMAT=<ID=PSTD,Number=1,Type=Float,Description="Position STD in reads"> ##FORMAT=<ID=QUAL,Number=1,Type=Float,Description="Mean quality score in reads"> ##FORMAT=<ID=QSTD,Number=1,Type=Float,Description="Quality score STD in reads"> ##FORMAT=<ID=SBF,Number=1,Type=Float,Description="Strand Bias Fisher p-value"> ##FORMAT=<ID=ODDRATIO,Number=1,Type=Float,Description="Strand Bias Odds ratio"> -##FORMAT=<ID=MQ,Number=1,Type=Float,Description="Mean Mapping Quality"> +##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="Mean Mapping Quality"> ##FORMAT=<ID=SN,Number=1,Type=Float,Description="Signal to noise"> ##FORMAT=<ID=HIAF,Number=1,Type=Float,Description="Allele frequency using only high quality bases"> ##FORMAT=<ID=NM,Number=1,Type=Float,Description="Mean mismatches in reads"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Tumor Normal chrM 150 . T C 121 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTCTTTGATTCCTGCCTCAT;RSEQ=CTATTATTTATCGCACCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:0,2:0,0:0,2:1:0,0:35:1:40.5:1:1:0:60:4:1:0:1.5 1/1:9:9:4,5:0,0:0,9:1:0,2:29.8:1:38.4:1:1:0:60:18:1:0.1111:1.8 chrM 195 . C T 120 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=1;VD=1;AF=1;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AATATTACAGGCGAACATAC;RSEQ=TACTAAAGTGTGTTAATTAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:0,1:0,0:0,1:1:0,0:22:0:40:0:1:0:60:2:1:0:2 1/1:9:9:3,6:0,0:0,9:1:0,2:21.9:1:37.9:1:1:0:60:18:1:0:1.8 -chrM 302 . AC A 85 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=Deletion;DP=0;VD=0;AF=0;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAACAAAAAATTTCCACCAA;RSEQ=CCCCCCCTCCCCCCGCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:5:5,0:1,0:1,5:0.8333:0,0:15.2:1:36.8:1:1:0:60:10:0.8333:0.5:1.6 +chrM 302 . AC A 85 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=Deletion;DP=0;VD=0;AF=0;SHIFT3=7;MSI=8.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAACAAAAAATTTCCACCAA;RSEQ=CCCCCCCTCCCCCCGCTTCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:5:5,0:1,0:1,5:0.8333:0,0:15.2:1:36.8:1:1:0:60:10:0.8333:0.5:1.6 chrM 410 . A T 149 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGATTTCAAATTTTATCTTT;RSEQ=GGCGGTATGCACTTTTAACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:3,0:0,0:0,3:1:0,0:23.3:1:36.7:1:1:0:60:6:1:0.3333:2.3 1/1:18:18:12,6:0,0:0,18:1:0,2:19.7:1:35.9:1:1:0:60:17:1:0.0556:1.9 -chrM 464 . C T 193 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=8;VD=8;AF=1;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.85965;SOR=Inf;LSEQ=TAACACATTATTTTCCCCTC;RSEQ=CACTCCCATACTACTAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:6,2:0,0:0,8:1:0,2:22.8:1:36.2:1:1:0:60:16:1:0:2.1 1/1:49:48:37,11:1,0:1,48:0.9796:0,2:24.9:1:34.6:1:1:0:60:15:0.9783:0.0408:2.2 -chrM 491 . T C 228 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=10;VD=10;AF=1;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.89474;SOR=Inf;LSEQ=CATACTACTAATCTCATCAA;RSEQ=ACAACCCCCGCCCATCCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:8,2:0,0:0,10:1:0,2:28.3:1:38.3:1:1:0:60:20:1:0:1.7 1/1:85:84:65,19:1,0:1,84:0.9882:0,2:21:1:35.7:1:1:0:60:27:0.9878:0.0824:1.7 +chrM 464 . C T 193 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=8;VD=8;AF=1;SHIFT3=2;MSI=3.000;MSILEN=1;SSF=0.85965;SOR=0;LSEQ=TAACACATTATTTTCCCCTC;RSEQ=CACTCCCATACTACTAATCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:8:8:6,2:0,0:0,8:1:0,2:22.8:1:36.2:1:1:0:60:16:1:0:2.1 1/1:49:48:37,11:1,0:1,48:0.9796:0,2:24.9:1:34.6:1:1:0:60:15:0.9783:0.0408:2.2 +chrM 491 . T C 228 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=10;VD=10;AF=1;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.89474;SOR=0;LSEQ=CATACTACTAATCTCATCAA;RSEQ=ACAACCCCCGCCCATCCTAC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:10:10:8,2:0,0:0,10:1:0,2:28.3:1:38.3:1:1:0:60:20:1:0:1.7 1/1:85:84:65,19:1,0:1,84:0.9882:0,2:21:1:35.7:1:1:0:60:27:0.9878:0.0824:1.7 chrM 1735 . C T 140 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACCTTAGCCAAACCATTTAC;RSEQ=CAAATAAAGTATAGGCGATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:1,2:0,0:0,3:1:0,2:46.7:1:40.3:1:1:0:60:6:1:0:1 1/1:14:14:6,8:0,0:0,14:1:0,2:26:1:37:1:1:0:60:28:1:0:1.1 chrM 2354 . C T 135 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CGCATAAGCCTGCGTCAGAT;RSEQ=AAAACACTGAACTGACAATT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:18.3:1:36.5:1:1:0:60:6:1:0.3333:1 1/1:11:11:8,3:0,0:0,11:1:0,2:23.1:1:39.1:1:1:0:60:22:1:0.0909:1.3 -chrM 2485 . C T 123 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTAAAAGGAACTCGGCAAA;RSEQ=CTTACCCCGCCTGTTTACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:17.7:1:37.7:1:1:0:53.3:6:1:0:1 1/1:13:13:8,5:0,0:0,13:1:0,2:29.4:1:33.5:1:1:0:40.2:5.5:1:0:1.2 -chrM 3012 . G A 99 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTTGGATCAGGACATCCC;RSEQ=ATGGTGCAGCCGCTATTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:1,5:0,0:0,6:1:0,2:36.7:1:38.5:1:1:0:58.2:12:1:0:1.2 -chrM 5581 . C T 133 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGCAATACTTAATTTCTG;RSEQ=AACAGCTAAGGACTGCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:12:12:2,10:0,0:0,12:1:0,2:24.8:1:37.3:1:1:0:33.6:24:1:0.0833:1 +chrM 2485 . C T 123 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGTAAAAGGAACTCGGCAAA;RSEQ=CTTACCCCGCCTGTTTACCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:2,1:0,0:0,3:1:0,2:17.7:1:37.7:1:1:0:53:6:1:0:1 1/1:13:13:8,5:0,0:0,13:1:0,2:29.4:1:33.5:1:1:0:40:5.5:1:0:1.2 +chrM 3012 . G A 99 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATGTTGGATCAGGACATCCC;RSEQ=ATGGTGCAGCCGCTATTAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:1,5:0,0:0,6:1:0,2:36.7:1:38.5:1:1:0:58:12:1:0:1.2 +chrM 5581 . C T 133 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTTGCAATACTTAATTTCTG;RSEQ=AACAGCTAAGGACTGCAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0 1/1:12:12:2,10:0,0:0,12:1:0,2:24.8:1:37.3:1:1:0:34:24:1:0.0833:1 chrM 8702 . G A 126 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAACCTCAAAACAAATGATA;RSEQ=CCATACACAACACTAAAGGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:46:1:34:1:1:0:60:4:1:0:1.5 1/1:11:11:6,5:0,0:0,11:1:0,2:25.2:1:36.7:1:1:0:51:22:1:0:1 -chrM 9378 . G A 110 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACTAACCATATACCAATG;RSEQ=TGGCGCGATGTAACACGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:20.3:1:36:1:1:0:46:6:1:0:1 1/1:9:9:4,5:0,0:0,9:1:0,2:19.7:1:34.9:1:1:0:44.3:8:1:0.1111:1.2 -chrM 11018 . C T 84 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCAACGCCACTTATCCAG;RSEQ=GAACCACTATCACGAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:2,3:0,0:0,5:1:0,2:29.6:1:36.4:1:1:0:51.2:10:1:0:1.2 +chrM 9378 . G A 110 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=3;VD=3;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACTAACCATATACCAATG;RSEQ=TGGCGCGATGTAACACGAGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:3:3:0,3:0,0:0,3:1:0,0:20.3:1:36:1:1:0:46:6:1:0:1 1/1:9:9:4,5:0,0:0,9:1:0,2:19.7:1:34.9:1:1:0:44:8:1:0.1111:1.2 +chrM 11018 . C T 84 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=2;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AGCCAACGCCACTTATCCAG;RSEQ=GAACCACTATCACGAAAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0 1/1:5:5:2,3:0,0:0,5:1:0,2:29.6:1:36.4:1:1:0:51:10:1:0:1.2 chrM 11252 . A G 150 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=5;VD=5;AF=1;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CTTCCCCTACTCATCGCACT;RSEQ=ATTTACACTCACAACACCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:1,4:0,0:0,5:1:0,2:26.2:1:37.4:1:1:0:60:10:1:0.2:1.2 1/1:17:17:9,8:0,0:0,17:1:0,2:27.8:1:36.9:1:1:0:60:34:1:0.0588:1.2 -chrM 11464 . T A 32 PASS STATUS=StrongSomatic;SAMPLE=Tumor;TYPE=SNV;DP=6;VD=2;AF=0.3333;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.125;SOR=Inf;LSEQ=AATAGTACTTGCCGCAGTAC;RSEQ=CTTAAAACTAGGCGGCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:25.5:1:32:1:1:1:60:4:0.3333:0:1 0/0:10:0:0,0:6,4:10,0:0:2,0:24.9:1:37:1:1:0:60:20:1:0:0.2 -chrM 11723 . C T 144 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCATAATCGCCCACGGACT;RSEQ=ACATCCTCATTACTATTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:16:16:8,8:0,0:0,16:1:0,2:30.1:1:36.2:1:1:0:50.4:32:1:0:1 -chrM 12613 . A G 106 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATAATATTCATCCCTGT;RSEQ=GCATTGTTCGTTACATGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:7:7:2,5:0,0:0,7:1:0,2:17.9:1:37.9:1:1:0:60:14:1:0:1.3 +chrM 11464 . T A 32 PASS STATUS=StrongSomatic;SAMPLE=Tumor;TYPE=SNV;DP=6;VD=2;AF=0.3333;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=0.125;SOR=0;LSEQ=AATAGTACTTGCCGCAGTAC;RSEQ=CTTAAAACTAGGCGGCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:25.5:1:32:1:1:1:60:4:0.3333:0:1 0/0:10:0:0,0:6,4:10,0:0:2,0:24.9:1:37:1:1:0:60:20:1:0:0.2 +chrM 11723 . C T 144 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=1;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=CTCATAATCGCCCACGGACT;RSEQ=ACATCCTCATTACTATTCTG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0 1/1:16:16:8,8:0,0:0,16:1:0,2:30.1:1:36.2:1:1:0:50:32:1:0:1 +chrM 12613 . A G 106 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TCCATAATATTCATCCCTGT;RSEQ=GCATTGTTCGTTACATGGTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0 1/1:7:7:2,5:0,0:0,7:1:0,2:17.9:1:37.9:1:1:0:60:14:1:0:1.3 chrM 12706 . T C 97 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=1;VD=1;AF=1;SHIFT3=0;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTCTTCAAATATCTACTCAT;RSEQ=TTCCTAATTACCATACTAAT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:39:0:40:0:1:0:60:2:1:0:1 1/1:6:6:4,2:0,0:0,6:1:0,2:28.7:1:37.7:1:1:0:60:12:1:0:1.3 chrM 12851 . G A 141 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=4;VD=4;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACACAGCAGCCATTCAAGCA;RSEQ=TCCTATACAACCGTATCGGC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:22.5:1:36.5:1:1:0:60:8:1:0:1 1/1:14:14:7,7:0,0:0,14:1:0,2:26.2:1:37.2:1:1:0:60:28:1:0:1.1 chrM 13709 . G A 103 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TAAACCCCATTAAACGCCTG;RSEQ=CAGCCGGAAGCCTATTCGCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:14.5:1:32:1:1:0:60:4:1:0:1 1/1:7:7:3,4:0,0:0,7:1:0,2:22.3:1:36.7:1:1:0:60:14:1:0:1 -chrM 14213 . C T 130 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAATGTTCAACCAGTAAC;RSEQ=ACTACTAATCAACGCCCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:11:11:5,6:0,0:0,11:1:0,2:25.2:1:37.7:1:1:0:58.1:22:1:0:1.2 -chrM 14581 . G A 141 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=5;VD=5;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCACACCGCTAACAATCA;RSEQ=TACTAAACCCCCATAAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1:0,2:24.8:1:37.4:1:1:0:43.6:10:1:0:1 1/1:15:15:9,6:0,0:0,15:1:0,2:31.5:1:36.1:1:1:0:56.3:14:1:0.0667:1 -chrM 14794 . A G 37 PASS STATUS=StrongSomatic;SAMPLE=Tumor;TYPE=SNV;DP=6;VD=2;AF=0.3333;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06494;SOR=Inf;LSEQ=CCTAATAAAATTAATTAACC;RSEQ=CTCATTCATCGACCTCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:23:1:37:1:1:1:60:4:0.3333:0.1667:1 0/0:16:0:0,0:6,10:16,0:0:2,0:22.6:1:30.3:1:1:0:60:15:1:0:0 +chrM 14213 . C T 130 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACAATGTTCAACCAGTAAC;RSEQ=ACTACTAATCAACGCCCATA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0 1/1:11:11:5,6:0,0:0,11:1:0,2:25.2:1:37.7:1:1:0:58:22:1:0:1.2 +chrM 14581 . G A 141 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=5;VD=5;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GACCACACCGCTAACAATCA;RSEQ=TACTAAACCCCCATAAATAG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:5:5:3,2:0,0:0,5:1:0,2:24.8:1:37.4:1:1:0:44:10:1:0:1 1/1:15:15:9,6:0,0:0,15:1:0,2:31.5:1:36.1:1:1:0:56:14:1:0.0667:1 +chrM 14794 . A G 37 PASS STATUS=StrongSomatic;SAMPLE=Tumor;TYPE=SNV;DP=6;VD=2;AF=0.3333;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=0.06494;SOR=0;LSEQ=CCTAATAAAATTAATTAACC;RSEQ=CTCATTCATCGACCTCCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/1:6:2:1,1:2,2:4,2:0.3333:2,2:23:1:37:1:1:1:60:4:0.3333:0.1667:1 0/0:16:0:0,0:6,10:16,0:0:2,0:22.6:1:30.3:1:1:0:60:15:1:0:0 chrM 14906 . A G 177 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=9;VD=9;AF=1;SHIFT3=0;MSI=2.000;MSILEN=2;SSF=1;SOR=0;LSEQ=ACAGGACTATTCCTAGCCAT;RSEQ=CACTACTCACCAGACGCCTC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:5,4:0,0:0,9:1:0,2:28.8:1:34.1:1:1:0:60:8:1:0.1111:2.1 1/1:33:33:15,18:0,0:0,33:1:0,2:22.5:1:35.2:1:1:0:60:66:1:0.0606:1.8 -chrM 14928 . A G 181 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=9;VD=9;AF=1;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.8;SOR=Inf;LSEQ=ACTACTCACCAGACGCCTCA;RSEQ=CCGCCTTTTCATCAATCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:5,4:0,0:0,9:1:0,2:30:1:38.8:1:1:0:60:18:1:0:2.1 1/1:36:35:16,19:0,1:1,35:0.9722:0,2:20.1:1:35.3:1:1:0:60:16.5:0.9706:0.0833:1.8 +chrM 14928 . A G 181 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=9;VD=9;AF=1;SHIFT3=1;MSI=2.000;MSILEN=1;SSF=0.8;SOR=0;LSEQ=ACTACTCACCAGACGCCTCA;RSEQ=CCGCCTTTTCATCAATCGCC GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:9:9:5,4:0,0:0,9:1:0,2:30:1:38.8:1:1:0:60:18:1:0:2.1 1/1:36:35:16,19:0,1:1,35:0.9722:0,2:20.1:1:35.3:1:1:0:60:16.5:0.9706:0.0833:1.8 chrM 15302 . A G 128 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=1;MSI=3.000;MSILEN=1;SSF=1;SOR=0;LSEQ=TTTACCTTTCACTTCATCTT;RSEQ=CCCTTCATTATTGCAGCCCT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:38:1:1:0:60:4:1:0:1 1/1:11:11:4,7:0,0:0,11:1:0,2:31.2:1:37.1:1:1:0:60:22:1:0:1.2 -chrM 15453 . C A 83 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTCGGCTTACTTCTCTTC;RSEQ=TTCTCTCCTTAATGACATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:3,3:0,0:0,6:1:0,2:22.7:1:32.2:1:1:0:60:12:1:0:1 -chrM 16070 . C T 107 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACCACCCAAGTATTGACT;RSEQ=ACCCATCAACAACCGCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0 1/1:7:7:4,3:0,0:0,7:1:0,2:27.4:1:38.4:1:1:0:60:14:1:0:1.7 +chrM 15453 . C A 83 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=CCCTCGGCTTACTTCTCTTC;RSEQ=TTCTCTCCTTAATGACATTA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0 1/1:6:6:3,3:0,0:0,6:1:0,2:22.7:1:32.2:1:1:0:60:12:1:0:1 +chrM 16070 . C T 107 PASS STATUS=Deletion;SAMPLE=Tumor;TYPE=SNV;DP=0;VD=0;AF=0;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACCACCCAAGTATTGACT;RSEQ=ACCCATCAACAACCGCTATG GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0 1/1:7:7:4,3:0,0:0,7:1:0,2:27.4:1:38.4:1:1:0:60:14:1:0:1.7 chrM 16127 . T C 85 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=1;VD=1;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GCCAGCCACCATGAATATTG;RSEQ=ACGGTACCATAAATACTTGA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:15:0:41:0:1:0:60:2:1:0:5 1/1:5:5:4,1:0,0:0,5:1:0,2:24.2:1:36.7:1:1:0:60:10:1:0.4:4.2 chrM 16146 . G A 106 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=1;VD=1;AF=1;SHIFT3=1;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=GTACGGTACCATAAATACTT;RSEQ=ACCACCTGTAGTACATAAAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:1:1:1,0:0,0:0,1:1:0,0:34:0:41:0:1:0:60:2:1:0:5 1/1:8:8:6,2:0,0:0,8:1:0,2:15.6:1:35.4:1:1:0:60:7:1:0.25:4.9 chrM 16184 . CC A 121 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=Complex;DP=2;VD=1;AF=0.5;SHIFT3=11;MSI=12.000;MSILEN=1;SSF=0.42308;SOR=0.2582;LSEQ=AAAACCCAACCCACATCAAA;RSEQ=CCCCCCCCCCATGCTTACAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:1,0:0,0:0,1:0.5:0,0:27:0:39:0:1:0:60:2:1:0:4 1/1:11:9:7,2:0,0:0,9:0.8182:0,2:28.2:1:38.2:1:1:0:60:18:0.9:0.1818:4.6 @@ -89,4 +90,4 @@ chrM 16224 . CT TC 159 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=Complex;DP=2;VD=1;AF=0.5;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=0.24901;SOR=0.12566;LSEQ=AAGCAAGTACAGCAATCAAC;RSEQ=TCAACTATCACACATCAACT GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/0:2:1:0,1:0,0:0,1:0.5:0,0:42:0:38:0:1:0:60:2:0.5:0:5 1/1:21:19:9,10:0,0:0,19:0.9048:0,2:26.4:1:37.6:1:1:0:60:38:1:0.0952:3.2 chrM 16263 . C T 158 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=4;VD=4;AF=1;SHIFT3=4;MSI=4.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACTGCAACTCCAAAGCCACC;RSEQ=CTCACCCACTAGGATACCAA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:4:4:2,2:0,0:0,4:1:0,2:25.8:1:34.2:1:1:0:60:3:1:0:3 1/1:18:18:9,9:0,0:0,18:1:0,2:26.9:1:38:1:1:0:60:36:1:0.0556:2.5 chrM 16322 . T C 125 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=1.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ACAGTACATAGTACATAAAG;RSEQ=CATTTACCGTACATAGCACA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:13.5:1:33.2:1:1:0:60:4:1:0.5:1.5 1/1:10:10:4,6:0,0:0,10:1:0,2:23.6:1:37.8:1:1:0:60:20:1:0:1.5 -chrM 16521 . C T 113 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGGTTCCTACTTCAGGG;RSEQ=CATAAAGCCTAAATAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:38:1:1:0:51.5:4:1:0:1 1/1:11:11:5,6:0,0:0,11:1:0,2:20.8:1:32.9:1:1:0:49.6:2.667:1:0.0909:1 +chrM 16521 . C T 113 PASS STATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=2.000;MSILEN=1;SSF=1;SOR=0;LSEQ=ATCTGGTTCCTACTTCAGGG;RSEQ=CATAAAGCCTAAATAGCCCA GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM 1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:38:1:1:0:52:4:1:0:1 1/1:11:11:5,6:0,0:0,11:1:0,2:20.8:1:32.9:1:1:0:50:2.667:1:0.0909:1
--- a/test-data/passed_variants_single.vcf Tue Aug 25 05:41:19 2020 -0400 +++ b/test-data/passed_variants_single.vcf Fri Sep 11 21:07:13 2020 +0000 @@ -1,4 +1,5 @@ -##fileformat=VCFv4.1 +##fileformat=VCFv4.3 +##source=VarDict_v1.8.1 ##INFO=<ID=SAMPLE,Number=1,Type=String,Description="Sample name (with whitespace translated to underscores)"> ##INFO=<ID=TYPE,Number=1,Type=String,Description="Variant Type: SNV Insertion Deletion Complex"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
--- a/vardict.xml Tue Aug 25 05:41:19 2020 -0400 +++ b/vardict.xml Fri Sep 11 21:07:13 2020 +0000 @@ -8,6 +8,7 @@ <requirement type="package" version="5.0.1">gawk</requirement> <requirement type="package" version="1.10">samtools</requirement> </requirements> + <expand macro="stdio" /> <command detect_errors="exit_code"><![CDATA[ #if $select_mode.mode == "paired" ln -s '$select_mode.normal' ./normal.bam &&