| Previous changeset 1:5f756651a1bc (2020-09-11) Next changeset 3:e0734e88a104 (2022-01-27) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit c247c47e1bc869c9094997f5052ce31367e10b1e" |
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modified:
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 |
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| diff -r 5f756651a1bc -r d262577e04b0 macros.xml --- a/macros.xml Fri Sep 11 21:07:13 2020 +0000 +++ b/macros.xml Tue Nov 16 19:05:56 2021 +0000 |
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| @@ -1,10 +1,10 @@ <macros> <token name="@VERSION_SUFFIX@">0</token> - <token name="@TOOL_VERSION@">1.8.1</token> + <token name="@TOOL_VERSION@">1.8.3</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"> - <option value="cached" selected="True">Use a built-in genome</option> + <option value="cached" selected="true">Use a built-in genome</option> <option value="history">Use a genome from the history</option> </param> <when value="cached"> |
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| diff -r 5f756651a1bc -r d262577e04b0 test-data/all_variants_paired.vcf --- a/test-data/all_variants_paired.vcf Fri Sep 11 21:07:13 2020 +0000 +++ b/test-data/all_variants_paired.vcf Tue Nov 16 19:05:56 2021 +0000 |
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| b'@@ -1,112 +1,112 @@\n-##fileformat=VCFv4.3\n-##source=VarDict_v1.8.1\n-##INFO=<ID=SAMPLE,Number=1,Type=String,Description="Sample name (with whitespace translated to underscores)">\n-##INFO=<ID=TYPE,Number=1,Type=String,Description="Variant Type: SNV Insertion Deletion Complex">\n-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">\n-##INFO=<ID=END,Number=1,Type=Integer,Description="Chr End Position">\n-##INFO=<ID=VD,Number=1,Type=Integer,Description="Variant Depth">\n-##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">\n-##INFO=<ID=SHIFT3,Number=1,Type=Integer,Description="No. of bases to be shifted to 3 prime for deletions due to alternative alignment">\n-##INFO=<ID=MSI,Number=1,Type=Float,Description="MicroSatellite. > 1 indicates MSI">\n-##INFO=<ID=MSILEN,Number=1,Type=Float,Description="MSI unit repeat length in bp">\n-##INFO=<ID=SSF,Number=1,Type=Float,Description="P-value">\n-##INFO=<ID=SOR,Number=1,Type=Float,Description="Odds ratio">\n-##INFO=<ID=LSEQ,Number=1,Type=String,Description="5\' flanking seq">\n-##INFO=<ID=RSEQ,Number=1,Type=String,Description="3\' flanking seq">\n-##INFO=<ID=STATUS,Number=1,Type=String,Description="Somatic or germline status">\n-##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)">\n-##INFO=<ID=InDelLikely,Number=0,Type=Flag,Description="Likely indels more than 2bp are not considered somatic (weak evidence of presence in normal samples)">\n-##FILTER=<ID=q22.5,Description="Mean Base Quality Below 22.5">\n-##FILTER=<ID=Q0,Description="Mean Mapping Quality Below 0">\n-##FILTER=<ID=p8,Description="Mean Position in Reads Less than 8">\n-##FILTER=<ID=SN1.5,Description="Signal to Noise Less than 1.5">\n-##FILTER=<ID=Bias,Description="Strand Bias">\n-##FILTER=<ID=pSTD,Description="Position in Reads has STD of 0">\n-##FILTER=<ID=MAF0.05,Description="Matched sample has AF > 0.05, thus not somatic">\n-##FILTER=<ID=d5,Description="Total Depth < 5">\n-##FILTER=<ID=v3,Description="Var Depth < 3">\n-##FILTER=<ID=f0.01,Description="Allele frequency < 0.01">\n-##FILTER=<ID=P0.05,Description="Not significant with p-value > 0.05">\n-##FILTER=<ID=DIFF0.2,Description="Non-somatic or LOH and allele frequency difference < 0.2">\n-##FILTER=<ID=MSI12,Description="Variant in MSI region with 12 non-monomer MSI or 12 monomer MSI">\n-##FILTER=<ID=NM5.25,Description="Mean mismatches in reads >= 5.25, thus likely false positive">\n-##FILTER=<ID=InGap,Description="The somatic variant is in the deletion gap, thus likely false positive">\n-##FILTER=<ID=InIns,Description="The somatic variant is adjacent to an insertion variant">\n-##FILTER=<ID=Cluster0bp,Description="Two somatic variants are within 0 bp">\n-##FILTER=<ID=LongAT,Description="The somatic variant is flanked by long A/T (>=14)">\n-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total Depth">\n-##FORMAT=<ID=VD,Number=1,Type=Integer,Description="Variant Depth">\n-##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n-##FORMAT=<ID=ALD,Number=2,Type=Integer,Description="Variant forward, reverse reads">\n-##FORMAT=<ID=RD,Number=2,Type=Integer,Description="Reference forward, reverse reads">\n-##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">\n-##FORMAT=<ID=ADJAF,Number=1,Type=Float,Description="Adjusted AF for indels due to local realignment">\n-##FORMAT=<ID=BIAS,Number=2,Type=String,Description="Strand Bias Info">\n-##FORMAT=<ID=PMEAN,Number=1,Type=Float,Description="Mean position in reads">\n-##FORMAT=<ID=PSTD,Number=1,Type=Float,Description="Position STD in reads">\n-##FORMAT=<ID=QUAL,Number=1,Type=Float,Description="Mean quality score in reads">\n-##FORMAT=<ID=QSTD,Number=1,Type=Float,Description="Quality score STD in reads">\n-##FORMAT=<ID=SBF,Number=1,Type=Float,Description="Strand Bias Fisher p-value">\n-##FORMAT=<ID=ODDRATIO,'..b'0;LSEQ=CCAGTCTTGTAAACCGGAGA;RSEQ=GAAAACCTTTTTCCAAGGAC\tGT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM\t0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0\t1/1:3:3:1,2:0,0:0,3:1:0,2:11.7:1:36:1:1:0:60:6:1:0:1\n+chrM\t16070\t\\.\tC\tT\t107\tPASS\tSTATUS=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\tGT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM\t0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0\t1/1:7:7:4,3:0,0:0,7:1:0,2:27.4:1:38.4:1:1:0:60:14:1:0:1.7\n+chrM\t16127\t\\.\tT\tC\t85\tPASS\tSTATUS=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\tGT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM\t1/1:1:1:1,0:0,0:0,1:1:0,0:15:0:41:0:1:0:60:2:1:0:5\t1/1:5:5:4,1:0,0:0,5:1:0,2:24.2:1:36.7:1:1:0:60:10:1:0.4:4.2\n+chrM\t16146\t\\.\tG\tA\t106\tPASS\tSTATUS=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\tGT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM\t1/1:1:1:1,0:0,0:0,1:1:0,0:34:0:41:0:1:0:60:2:1:0:5\t1/1:8:8:6,2:0,0:0,8:1:0,2:15.6:1:35.4:1:1:0:60:7:1:0.25:4.9\n+chrM\t16173\t\\.\tC\tT\t120\td5;v3;NM5.25\tSTATUS=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\tGT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM\t1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:37.5:1:1:0:60:4:1:0:5.5\t1/1:10:10:6,4:0,0:0,10:1:0,2:26.6:1:36.2:1:1:0:60:20:1:0:5.4\n+chrM\t16184\t\\.\tCC\tA\t121\tPASS\tSTATUS=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\tGT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM\t1/0:2:1:1,0:0,0:0,1:0.5:0,0:27:0:39:0:1:0:60:2:1:0:4\t1/1:11:9:7,2:0,0:0,9:0.8182:0,2:28.2:1:38.2:1:1:0:60:18:0.9:0.1818:4.6\n+chrM\t16191\t\\.\tC\tT\t124\tPASS\tSTATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACCCACATCAAACCCCCCC;RSEQ=CCCCATGCTTACAAGCAAGT\tGT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM\t1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:33.5:1:1:0:60:4:1:0:5.5\t1/1:12:12:7,5:0,0:0,12:1:0,2:29.6:1:34.7:1:1:0:60:11:1:0.0833:5.2\n+chrM\t16224\t\\.\tCT\tTC\t159\tPASS\tSTATUS=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\tGT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM\t1/0:2:1:0,1:0,0:0,1:0.5:0,0:42:0:38:0:1:0:60:2:0.5:0:5\t1/1:21:19:9,10:0,0:0,19:0.9048:0,2:26.4:1:37.6:1:1:0:60:38:1:0.0952:3.2\n+chrM\t16263\t\\.\tC\tT\t158\tPASS\tSTATUS=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\tGT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM\t1/1:4:4:2,2:0,0:0,4:1:0,2:25.8:1:34.2:1:1:0:60:3:1:0:3\t1/1:18:18:9,9:0,0:0,18:1:0,2:26.9:1:38:1:1:0:60:36:1:0.0556:2.5\n+chrM\t16322\t\\.\tT\tC\t125\tPASS\tSTATUS=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\tGT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM\t1/1:2:2:1,1:0,0:0,2:1:0,2:13.5:1:33.2:1:1:0:60:4:1:0.5:1.5\t1/1:10:10:4,6:0,0:0,10:1:0,2:23.6:1:37.8:1:1:0:60:20:1:0:1.5\n+chrM\t16521\t\\.\tC\tT\t113\tPASS\tSTATUS=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\tGT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM\t1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:38:1:1:0:52:4:1:0:1\t1/1:11:11:5,6:0,0:0,11:1:0,2:20.8:1:32.9:1:1:0:50:2.667:1:0.0909:1\n' 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| diff -r 5f756651a1bc -r d262577e04b0 test-data/all_variants_single.vcf --- a/test-data/all_variants_single.vcf Fri Sep 11 21:07:13 2020 +0000 +++ b/test-data/all_variants_single.vcf Tue Nov 16 19:05:56 2021 +0000 |
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| b'@@ -1,92 +1,92 @@\n-##fileformat=VCFv4.3\n-##source=VarDict_v1.8.1\n-##INFO=<ID=SAMPLE,Number=1,Type=String,Description="Sample name (with whitespace translated to underscores)">\n-##INFO=<ID=TYPE,Number=1,Type=String,Description="Variant Type: SNV Insertion Deletion Complex">\n-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">\n-##INFO=<ID=END,Number=1,Type=Integer,Description="Chr End Position">\n-##INFO=<ID=VD,Number=1,Type=Integer,Description="Variant Depth">\n-##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">\n-##INFO=<ID=BIAS,Number=1,Type=String,Description="Strand Bias Info">\n-##INFO=<ID=REFBIAS,Number=1,Type=String,Description="Reference depth by strand">\n-##INFO=<ID=VARBIAS,Number=1,Type=String,Description="Variant depth by strand">\n-##INFO=<ID=PMEAN,Number=1,Type=Float,Description="Mean position in reads">\n-##INFO=<ID=PSTD,Number=1,Type=Float,Description="Position STD in reads">\n-##INFO=<ID=QUAL,Number=1,Type=Float,Description="Mean quality score in reads">\n-##INFO=<ID=QSTD,Number=1,Type=Float,Description="Quality score STD in reads">\n-##INFO=<ID=SBF,Number=1,Type=Float,Description="Strand Bias Fisher p-value">\n-##INFO=<ID=ODDRATIO,Number=1,Type=Float,Description="Strand Bias Odds ratio">\n-##INFO=<ID=MQ,Number=1,Type=Float,Description="Mean Mapping Quality">\n-##INFO=<ID=SN,Number=1,Type=Float,Description="Signal to noise">\n-##INFO=<ID=HIAF,Number=1,Type=Float,Description="Allele frequency using only high quality bases">\n-##INFO=<ID=ADJAF,Number=1,Type=Float,Description="Adjusted AF for indels due to local realignment">\n-##INFO=<ID=SHIFT3,Number=1,Type=Integer,Description="No. of bases to be shifted to 3 prime for deletions due to alternative alignment">\n-##INFO=<ID=MSI,Number=1,Type=Float,Description="MicroSatellite. > 1 indicates MSI">\n-##INFO=<ID=MSILEN,Number=1,Type=Float,Description="MicroSatellite unit length in bp">\n-##INFO=<ID=NM,Number=1,Type=Float,Description="Mean mismatches in reads">\n-##INFO=<ID=LSEQ,Number=1,Type=String,Description="5\' flanking seq">\n-##INFO=<ID=RSEQ,Number=1,Type=String,Description="3\' flanking seq">\n-##INFO=<ID=GDAMP,Number=1,Type=Integer,Description="No. of amplicons supporting variant">\n-##INFO=<ID=TLAMP,Number=1,Type=Integer,Description="Total of amplicons covering variant">\n-##INFO=<ID=NCAMP,Number=1,Type=Integer,Description="No. of amplicons don\'t work">\n-##INFO=<ID=AMPFLAG,Number=1,Type=Integer,Description="Top variant in amplicons don\'t match">\n-##INFO=<ID=HICNT,Number=1,Type=Integer,Description="High quality variant reads">\n-##INFO=<ID=HICOV,Number=1,Type=Integer,Description="High quality total reads">\n-##INFO=<ID=SPLITREAD,Number=1,Type=Integer,Description="No. of split reads supporting SV">\n-##INFO=<ID=SPANPAIR,Number=1,Type=Integer,Description="No. of pairs supporting SV">\n-##INFO=<ID=SVTYPE,Number=1,Type=String,Description="SV type: INV DUP DEL INS FUS">\n-##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="The length of SV in bp">\n-##INFO=<ID=DUPRATE,Number=1,Type=Float,Description="Duplication rate in fraction">\n-##FILTER=<ID=q22.5,Description="Mean Base Quality Below 22.5">\n-##FILTER=<ID=Q10,Description="Mean Mapping Quality Below 10">\n-##FILTER=<ID=p8,Description="Mean Position in Reads Less than 8">\n-##FILTER=<ID=SN1.5,Description="Signal to Noise Less than 1.5">\n-##FILTER=<ID=Bias,Description="Strand Bias">\n-##FILTER=<ID=pSTD,Description="Position in Reads has STD of 0">\n-##FILTER=<ID=d3,Description="Total Depth < 3">\n-##FILTER=<ID=v2,Description="Var Depth < 2">\n-##FILTER=<ID=f0.01,Description="Allele frequency < 0.01">\n-##FILTER=<ID=MSI12,Description="Variant in MSI region with 12 non-monomer MSI or 13 monomer MSI">\n-##FILTER=<ID=NM5.25,Description="Mean mismatches in reads >= 5.25, thus likely false positive">\n-##FILTER=<ID=InGap,Description="The variant is in the deletion gap, thus likely false positive">\n-##FILTER=<ID=InIns,Description="The variant is adjacent to an insertion variant">\n-##FILTER=<ID=Cluster0bp,Description="Two variants are wi'..b'ANPAIR=0\tGT:DP:VD:AD:AF:RD:ALD\t1/1:4:4:0,4:1:0,0:2,2\n+chrM\t13709\t\\.\tG\tA\t32\tPASS\tSAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=14.5;PSTD=1;QUAL=32;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=TAAACCCCATTAAACGCCTG;RSEQ=CAGCCGGAAGCCTATTCGCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0\tGT:DP:VD:AD:AF:RD:ALD\t1/1:2:2:0,2:1:0,0:1,1\n+chrM\t14581\t\\.\tG\tA\t86\tPASS\tSAMPLE=Sample;TYPE=SNV;DP=5;VD=5;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=3:2;PMEAN=24.8;PSTD=1;QUAL=37.4;QSTD=1;SBF=1;ODDRATIO=0;MQ=43.6;SN=10;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=5;HICOV=5;LSEQ=GACCACACCGCTAACAATCA;RSEQ=TACTAAACCCCCATAAATAG;DUPRATE=0;SPLITREAD=0;SPANPAIR=0\tGT:DP:VD:AD:AF:RD:ALD\t1/1:5:5:0,5:1:0,0:3,2\n+chrM\t14794\t\\.\tA\tG\t37\tPASS\tSAMPLE=Sample;TYPE=SNV;DP=6;VD=2;AF=0.3333;BIAS=2:2;REFBIAS=2:2;VARBIAS=1:1;PMEAN=23;PSTD=1;QUAL=37;QSTD=1;SBF=1;ODDRATIO=1;MQ=60;SN=4;HIAF=0.3333;ADJAF=0.1667;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=2;HICOV=6;LSEQ=CCTAATAAAATTAATTAACC;RSEQ=CTCATTCATCGACCTCCCCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0\tGT:DP:VD:AD:AF:RD:ALD\t0/1:6:2:4,2:0.3333:2,2:1,1\n+chrM\t14906\t\\.\tA\tG\t108\tPASS\tSAMPLE=Sample;TYPE=SNV;DP=9;VD=9;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=5:4;PMEAN=28.8;PSTD=1;QUAL=34.1;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=8;HIAF=1.0000;ADJAF=0.1111;SHIFT3=0;MSI=2;MSILEN=2;NM=2.1;HICNT=8;HICOV=8;LSEQ=ACAGGACTATTCCTAGCCAT;RSEQ=CACTACTCACCAGACGCCTC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0\tGT:DP:VD:AD:AF:RD:ALD\t1/1:9:9:0,9:1:0,0:5,4\n+chrM\t14928\t\\.\tA\tG\t122\tPASS\tSAMPLE=Sample;TYPE=SNV;DP=9;VD=9;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=5:4;PMEAN=30;PSTD=1;QUAL=38.8;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=18;HIAF=1.0000;ADJAF=0;SHIFT3=1;MSI=2;MSILEN=1;NM=2.1;HICNT=9;HICOV=9;LSEQ=ACTACTCACCAGACGCCTCA;RSEQ=CCGCCTTTTCATCAATCGCC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0\tGT:DP:VD:AD:AF:RD:ALD\t1/1:9:9:0,9:1:0,0:5,4\n+chrM\t15302\t\\.\tA\tG\t38\tPASS\tSAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=26.5;PSTD=1;QUAL=38;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=1;MSI=3;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=TTTACCTTTCACTTCATCTT;RSEQ=CCCTTCATTATTGCAGCCCT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0\tGT:DP:VD:AD:AF:RD:ALD\t1/1:2:2:0,2:1:0,0:1,1\n+chrM\t16173\t\\.\tC\tT\t37\tNM5.25\tSAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=22;PSTD=1;QUAL=37.5;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=1;MSI=3;MSILEN=1;NM=5.5;HICNT=2;HICOV=2;LSEQ=TGTAGTACATAAAAACCCAA;RSEQ=CCACATCAAACCCCCCCCCC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0\tGT:DP:VD:AD:AF:RD:ALD\t1/1:2:2:0,2:1:0,0:1,1\n+chrM\t16191\t\\.\tC\tT\t33\tNM5.25\tSAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=22;PSTD=1;QUAL=33.5;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=12;MSILEN=1;NM=5.5;HICNT=2;HICOV=2;LSEQ=AACCCACATCAAACCCCCCC;RSEQ=CCCCATGCTTACAAGCAAGT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0\tGT:DP:VD:AD:AF:RD:ALD\t1/1:2:2:0,2:1:0,0:1,1\n+chrM\t16263\t\\.\tC\tT\t68\tPASS\tSAMPLE=Sample;TYPE=SNV;DP=4;VD=4;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=2:2;PMEAN=25.8;PSTD=1;QUAL=34.2;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=3;HIAF=1.0000;ADJAF=0;SHIFT3=4;MSI=4;MSILEN=1;NM=3.0;HICNT=3;HICOV=3;LSEQ=ACTGCAACTCCAAAGCCACC;RSEQ=CTCACCCACTAGGATACCAA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0\tGT:DP:VD:AD:AF:RD:ALD\t1/1:4:4:0,4:1:0,0:2,2\n+chrM\t16322\t\\.\tT\tC\t33\tPASS\tSAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=13.5;PSTD=1;QUAL=33.2;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0.5;SHIFT3=0;MSI=1;MSILEN=1;NM=1.5;HICNT=2;HICOV=2;LSEQ=ACAGTACATAGTACATAAAG;RSEQ=CATTTACCGTACATAGCACA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0\tGT:DP:VD:AD:AF:RD:ALD\t1/1:2:2:0,2:1:0,0:1,1\n+chrM\t16521\t\\.\tC\tT\t38\tPASS\tSAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=33.5;PSTD=1;QUAL=38;QSTD=1;SBF=1;ODDRATIO=0;MQ=51.5;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=2;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=ATCTGGTTCCTACTTCAGGG;RSEQ=CATAAAGCCTAAATAGCCCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0\tGT:DP:VD:AD:AF:RD:ALD\t1/1:2:2:0,2:1:0,0:1,1\n' |
| b |
| diff -r 5f756651a1bc -r d262577e04b0 test-data/passed_variants_paired.vcf --- a/test-data/passed_variants_paired.vcf Fri Sep 11 21:07:13 2020 +0000 +++ b/test-data/passed_variants_paired.vcf Tue Nov 16 19:05:56 2021 +0000 |
| b |
| b'@@ -1,93 +1,93 @@\n-##fileformat=VCFv4.3\n-##source=VarDict_v1.8.1\n-##INFO=<ID=SAMPLE,Number=1,Type=String,Description="Sample name (with whitespace translated to underscores)">\n-##INFO=<ID=TYPE,Number=1,Type=String,Description="Variant Type: SNV Insertion Deletion Complex">\n-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">\n-##INFO=<ID=END,Number=1,Type=Integer,Description="Chr End Position">\n-##INFO=<ID=VD,Number=1,Type=Integer,Description="Variant Depth">\n-##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">\n-##INFO=<ID=SHIFT3,Number=1,Type=Integer,Description="No. of bases to be shifted to 3 prime for deletions due to alternative alignment">\n-##INFO=<ID=MSI,Number=1,Type=Float,Description="MicroSatellite. > 1 indicates MSI">\n-##INFO=<ID=MSILEN,Number=1,Type=Float,Description="MSI unit repeat length in bp">\n-##INFO=<ID=SSF,Number=1,Type=Float,Description="P-value">\n-##INFO=<ID=SOR,Number=1,Type=Float,Description="Odds ratio">\n-##INFO=<ID=LSEQ,Number=1,Type=String,Description="5\' flanking seq">\n-##INFO=<ID=RSEQ,Number=1,Type=String,Description="3\' flanking seq">\n-##INFO=<ID=STATUS,Number=1,Type=String,Description="Somatic or germline status">\n-##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)">\n-##INFO=<ID=InDelLikely,Number=0,Type=Flag,Description="Likely indels more than 2bp are not considered somatic (weak evidence of presence in normal samples)">\n-##FILTER=<ID=q22.5,Description="Mean Base Quality Below 22.5">\n-##FILTER=<ID=Q0,Description="Mean Mapping Quality Below 0">\n-##FILTER=<ID=p8,Description="Mean Position in Reads Less than 8">\n-##FILTER=<ID=SN1.5,Description="Signal to Noise Less than 1.5">\n-##FILTER=<ID=Bias,Description="Strand Bias">\n-##FILTER=<ID=pSTD,Description="Position in Reads has STD of 0">\n-##FILTER=<ID=MAF0.05,Description="Matched sample has AF > 0.05, thus not somatic">\n-##FILTER=<ID=d5,Description="Total Depth < 5">\n-##FILTER=<ID=v3,Description="Var Depth < 3">\n-##FILTER=<ID=f0.01,Description="Allele frequency < 0.01">\n-##FILTER=<ID=P0.05,Description="Not significant with p-value > 0.05">\n-##FILTER=<ID=DIFF0.2,Description="Non-somatic or LOH and allele frequency difference < 0.2">\n-##FILTER=<ID=MSI12,Description="Variant in MSI region with 12 non-monomer MSI or 12 monomer MSI">\n-##FILTER=<ID=NM5.25,Description="Mean mismatches in reads >= 5.25, thus likely false positive">\n-##FILTER=<ID=InGap,Description="The somatic variant is in the deletion gap, thus likely false positive">\n-##FILTER=<ID=InIns,Description="The somatic variant is adjacent to an insertion variant">\n-##FILTER=<ID=Cluster0bp,Description="Two somatic variants are within 0 bp">\n-##FILTER=<ID=LongAT,Description="The somatic variant is flanked by long A/T (>=14)">\n-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total Depth">\n-##FORMAT=<ID=VD,Number=1,Type=Integer,Description="Variant Depth">\n-##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n-##FORMAT=<ID=ALD,Number=2,Type=Integer,Description="Variant forward, reverse reads">\n-##FORMAT=<ID=RD,Number=2,Type=Integer,Description="Reference forward, reverse reads">\n-##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">\n-##FORMAT=<ID=ADJAF,Number=1,Type=Float,Description="Adjusted AF for indels due to local realignment">\n-##FORMAT=<ID=BIAS,Number=2,Type=String,Description="Strand Bias Info">\n-##FORMAT=<ID=PMEAN,Number=1,Type=Float,Description="Mean position in reads">\n-##FORMAT=<ID=PSTD,Number=1,Type=Float,Description="Position STD in reads">\n-##FORMAT=<ID=QUAL,Number=1,Type=Float,Description="Mean quality score in reads">\n-##FORMAT=<ID=QSTD,Number=1,Type=Float,Description="Quality score STD in reads">\n-##FORMAT=<ID=SBF,Number=1,Type=Float,Description="Strand Bias Fisher p-value">\n-##FORMAT=<ID=ODDRATIO,Nu'..b'F=1;SOR=0;LSEQ=TTTACCTTTCACTTCATCTT;RSEQ=CCCTTCATTATTGCAGCCCT\tGT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM\t1/1:2:2:1,1:0,0:0,2:1:0,2:26.5:1:38:1:1:0:60:4:1:0:1\t1/1:11:11:4,7:0,0:0,11:1:0,2:31.2:1:37.1:1:1:0:60:22:1:0:1.2\n+chrM\t15453\t\\.\tC\tA\t83\tPASS\tSTATUS=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\tGT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM\t0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0\t1/1:6:6:3,3:0,0:0,6:1:0,2:22.7:1:32.2:1:1:0:60:12:1:0:1\n+chrM\t16070\t\\.\tC\tT\t107\tPASS\tSTATUS=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\tGT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM\t0/0:0:0:0,0:0,0:0,0:0:0,0:0:0:0:0:1:0:0:0:0:0:0\t1/1:7:7:4,3:0,0:0,7:1:0,2:27.4:1:38.4:1:1:0:60:14:1:0:1.7\n+chrM\t16127\t\\.\tT\tC\t85\tPASS\tSTATUS=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\tGT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM\t1/1:1:1:1,0:0,0:0,1:1:0,0:15:0:41:0:1:0:60:2:1:0:5\t1/1:5:5:4,1:0,0:0,5:1:0,2:24.2:1:36.7:1:1:0:60:10:1:0.4:4.2\n+chrM\t16146\t\\.\tG\tA\t106\tPASS\tSTATUS=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\tGT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM\t1/1:1:1:1,0:0,0:0,1:1:0,0:34:0:41:0:1:0:60:2:1:0:5\t1/1:8:8:6,2:0,0:0,8:1:0,2:15.6:1:35.4:1:1:0:60:7:1:0.25:4.9\n+chrM\t16184\t\\.\tCC\tA\t121\tPASS\tSTATUS=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\tGT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM\t1/0:2:1:1,0:0,0:0,1:0.5:0,0:27:0:39:0:1:0:60:2:1:0:4\t1/1:11:9:7,2:0,0:0,9:0.8182:0,2:28.2:1:38.2:1:1:0:60:18:0.9:0.1818:4.6\n+chrM\t16191\t\\.\tC\tT\t124\tPASS\tSTATUS=Germline;SAMPLE=Tumor;TYPE=SNV;DP=2;VD=2;AF=1;SHIFT3=0;MSI=12.000;MSILEN=1;SSF=1;SOR=0;LSEQ=AACCCACATCAAACCCCCCC;RSEQ=CCCCATGCTTACAAGCAAGT\tGT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM\t1/1:2:2:1,1:0,0:0,2:1:0,2:22:1:33.5:1:1:0:60:4:1:0:5.5\t1/1:12:12:7,5:0,0:0,12:1:0,2:29.6:1:34.7:1:1:0:60:11:1:0.0833:5.2\n+chrM\t16224\t\\.\tCT\tTC\t159\tPASS\tSTATUS=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\tGT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM\t1/0:2:1:0,1:0,0:0,1:0.5:0,0:42:0:38:0:1:0:60:2:0.5:0:5\t1/1:21:19:9,10:0,0:0,19:0.9048:0,2:26.4:1:37.6:1:1:0:60:38:1:0.0952:3.2\n+chrM\t16263\t\\.\tC\tT\t158\tPASS\tSTATUS=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\tGT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM\t1/1:4:4:2,2:0,0:0,4:1:0,2:25.8:1:34.2:1:1:0:60:3:1:0:3\t1/1:18:18:9,9:0,0:0,18:1:0,2:26.9:1:38:1:1:0:60:36:1:0.0556:2.5\n+chrM\t16322\t\\.\tT\tC\t125\tPASS\tSTATUS=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\tGT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM\t1/1:2:2:1,1:0,0:0,2:1:0,2:13.5:1:33.2:1:1:0:60:4:1:0.5:1.5\t1/1:10:10:4,6:0,0:0,10:1:0,2:23.6:1:37.8:1:1:0:60:20:1:0:1.5\n+chrM\t16521\t\\.\tC\tT\t113\tPASS\tSTATUS=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\tGT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM\t1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:38:1:1:0:52:4:1:0:1\t1/1:11:11:5,6:0,0:0,11:1:0,2:20.8:1:32.9:1:1:0:50:2.667:1:0.0909:1\n' |
| b |
| diff -r 5f756651a1bc -r d262577e04b0 test-data/passed_variants_single.vcf --- a/test-data/passed_variants_single.vcf Fri Sep 11 21:07:13 2020 +0000 +++ b/test-data/passed_variants_single.vcf Tue Nov 16 19:05:56 2021 +0000 |
| b |
| b'@@ -1,90 +1,90 @@\n-##fileformat=VCFv4.3\n-##source=VarDict_v1.8.1\n-##INFO=<ID=SAMPLE,Number=1,Type=String,Description="Sample name (with whitespace translated to underscores)">\n-##INFO=<ID=TYPE,Number=1,Type=String,Description="Variant Type: SNV Insertion Deletion Complex">\n-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">\n-##INFO=<ID=END,Number=1,Type=Integer,Description="Chr End Position">\n-##INFO=<ID=VD,Number=1,Type=Integer,Description="Variant Depth">\n-##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">\n-##INFO=<ID=BIAS,Number=1,Type=String,Description="Strand Bias Info">\n-##INFO=<ID=REFBIAS,Number=1,Type=String,Description="Reference depth by strand">\n-##INFO=<ID=VARBIAS,Number=1,Type=String,Description="Variant depth by strand">\n-##INFO=<ID=PMEAN,Number=1,Type=Float,Description="Mean position in reads">\n-##INFO=<ID=PSTD,Number=1,Type=Float,Description="Position STD in reads">\n-##INFO=<ID=QUAL,Number=1,Type=Float,Description="Mean quality score in reads">\n-##INFO=<ID=QSTD,Number=1,Type=Float,Description="Quality score STD in reads">\n-##INFO=<ID=SBF,Number=1,Type=Float,Description="Strand Bias Fisher p-value">\n-##INFO=<ID=ODDRATIO,Number=1,Type=Float,Description="Strand Bias Odds ratio">\n-##INFO=<ID=MQ,Number=1,Type=Float,Description="Mean Mapping Quality">\n-##INFO=<ID=SN,Number=1,Type=Float,Description="Signal to noise">\n-##INFO=<ID=HIAF,Number=1,Type=Float,Description="Allele frequency using only high quality bases">\n-##INFO=<ID=ADJAF,Number=1,Type=Float,Description="Adjusted AF for indels due to local realignment">\n-##INFO=<ID=SHIFT3,Number=1,Type=Integer,Description="No. of bases to be shifted to 3 prime for deletions due to alternative alignment">\n-##INFO=<ID=MSI,Number=1,Type=Float,Description="MicroSatellite. > 1 indicates MSI">\n-##INFO=<ID=MSILEN,Number=1,Type=Float,Description="MicroSatellite unit length in bp">\n-##INFO=<ID=NM,Number=1,Type=Float,Description="Mean mismatches in reads">\n-##INFO=<ID=LSEQ,Number=1,Type=String,Description="5\' flanking seq">\n-##INFO=<ID=RSEQ,Number=1,Type=String,Description="3\' flanking seq">\n-##INFO=<ID=GDAMP,Number=1,Type=Integer,Description="No. of amplicons supporting variant">\n-##INFO=<ID=TLAMP,Number=1,Type=Integer,Description="Total of amplicons covering variant">\n-##INFO=<ID=NCAMP,Number=1,Type=Integer,Description="No. of amplicons don\'t work">\n-##INFO=<ID=AMPFLAG,Number=1,Type=Integer,Description="Top variant in amplicons don\'t match">\n-##INFO=<ID=HICNT,Number=1,Type=Integer,Description="High quality variant reads">\n-##INFO=<ID=HICOV,Number=1,Type=Integer,Description="High quality total reads">\n-##INFO=<ID=SPLITREAD,Number=1,Type=Integer,Description="No. of split reads supporting SV">\n-##INFO=<ID=SPANPAIR,Number=1,Type=Integer,Description="No. of pairs supporting SV">\n-##INFO=<ID=SVTYPE,Number=1,Type=String,Description="SV type: INV DUP DEL INS FUS">\n-##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="The length of SV in bp">\n-##INFO=<ID=DUPRATE,Number=1,Type=Float,Description="Duplication rate in fraction">\n-##FILTER=<ID=q22.5,Description="Mean Base Quality Below 22.5">\n-##FILTER=<ID=Q10,Description="Mean Mapping Quality Below 10">\n-##FILTER=<ID=p8,Description="Mean Position in Reads Less than 8">\n-##FILTER=<ID=SN1.5,Description="Signal to Noise Less than 1.5">\n-##FILTER=<ID=Bias,Description="Strand Bias">\n-##FILTER=<ID=pSTD,Description="Position in Reads has STD of 0">\n-##FILTER=<ID=d3,Description="Total Depth < 3">\n-##FILTER=<ID=v2,Description="Var Depth < 2">\n-##FILTER=<ID=f0.01,Description="Allele frequency < 0.01">\n-##FILTER=<ID=MSI12,Description="Variant in MSI region with 12 non-monomer MSI or 13 monomer MSI">\n-##FILTER=<ID=NM5.25,Description="Mean mismatches in reads >= 5.25, thus likely false positive">\n-##FILTER=<ID=InGap,Description="The variant is in the deletion gap, thus likely false positive">\n-##FILTER=<ID=InIns,Description="The variant is adjacent to an insertion variant">\n-##FILTER=<ID=Cluster0bp,Description="Two variants are wi'..b'0\tGT:DP:VD:AD:AF:RD:ALD\t1/1:5:5:0,5:1:0,0:1,4\n+chrM\t11464\t\\.\tT\tA\t32\tPASS\tSAMPLE=Sample;TYPE=SNV;DP=6;VD=2;AF=0.3333;BIAS=2:2;REFBIAS=2:2;VARBIAS=1:1;PMEAN=25.5;PSTD=1;QUAL=32;QSTD=1;SBF=1;ODDRATIO=1;MQ=60;SN=4;HIAF=0.3333;ADJAF=0;SHIFT3=1;MSI=1;MSILEN=1;NM=1.0;HICNT=2;HICOV=6;LSEQ=AATAGTACTTGCCGCAGTAC;RSEQ=CTTAAAACTAGGCGGCTATG;DUPRATE=0;SPLITREAD=0;SPANPAIR=0\tGT:DP:VD:AD:AF:RD:ALD\t0/1:6:2:4,2:0.3333:2,2:1,1\n+chrM\t12851\t\\.\tG\tA\t73\tPASS\tSAMPLE=Sample;TYPE=SNV;DP=4;VD=4;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=2:2;PMEAN=22.5;PSTD=1;QUAL=36.5;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=8;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=4;HICOV=4;LSEQ=ACACAGCAGCCATTCAAGCA;RSEQ=TCCTATACAACCGTATCGGC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0\tGT:DP:VD:AD:AF:RD:ALD\t1/1:4:4:0,4:1:0,0:2,2\n+chrM\t13709\t\\.\tG\tA\t32\tPASS\tSAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=14.5;PSTD=1;QUAL=32;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=TAAACCCCATTAAACGCCTG;RSEQ=CAGCCGGAAGCCTATTCGCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0\tGT:DP:VD:AD:AF:RD:ALD\t1/1:2:2:0,2:1:0,0:1,1\n+chrM\t14581\t\\.\tG\tA\t86\tPASS\tSAMPLE=Sample;TYPE=SNV;DP=5;VD=5;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=3:2;PMEAN=24.8;PSTD=1;QUAL=37.4;QSTD=1;SBF=1;ODDRATIO=0;MQ=43.6;SN=10;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=5;HICOV=5;LSEQ=GACCACACCGCTAACAATCA;RSEQ=TACTAAACCCCCATAAATAG;DUPRATE=0;SPLITREAD=0;SPANPAIR=0\tGT:DP:VD:AD:AF:RD:ALD\t1/1:5:5:0,5:1:0,0:3,2\n+chrM\t14794\t\\.\tA\tG\t37\tPASS\tSAMPLE=Sample;TYPE=SNV;DP=6;VD=2;AF=0.3333;BIAS=2:2;REFBIAS=2:2;VARBIAS=1:1;PMEAN=23;PSTD=1;QUAL=37;QSTD=1;SBF=1;ODDRATIO=1;MQ=60;SN=4;HIAF=0.3333;ADJAF=0.1667;SHIFT3=0;MSI=1;MSILEN=1;NM=1.0;HICNT=2;HICOV=6;LSEQ=CCTAATAAAATTAATTAACC;RSEQ=CTCATTCATCGACCTCCCCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0\tGT:DP:VD:AD:AF:RD:ALD\t0/1:6:2:4,2:0.3333:2,2:1,1\n+chrM\t14906\t\\.\tA\tG\t108\tPASS\tSAMPLE=Sample;TYPE=SNV;DP=9;VD=9;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=5:4;PMEAN=28.8;PSTD=1;QUAL=34.1;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=8;HIAF=1.0000;ADJAF=0.1111;SHIFT3=0;MSI=2;MSILEN=2;NM=2.1;HICNT=8;HICOV=8;LSEQ=ACAGGACTATTCCTAGCCAT;RSEQ=CACTACTCACCAGACGCCTC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0\tGT:DP:VD:AD:AF:RD:ALD\t1/1:9:9:0,9:1:0,0:5,4\n+chrM\t14928\t\\.\tA\tG\t122\tPASS\tSAMPLE=Sample;TYPE=SNV;DP=9;VD=9;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=5:4;PMEAN=30;PSTD=1;QUAL=38.8;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=18;HIAF=1.0000;ADJAF=0;SHIFT3=1;MSI=2;MSILEN=1;NM=2.1;HICNT=9;HICOV=9;LSEQ=ACTACTCACCAGACGCCTCA;RSEQ=CCGCCTTTTCATCAATCGCC;DUPRATE=0;SPLITREAD=0;SPANPAIR=0\tGT:DP:VD:AD:AF:RD:ALD\t1/1:9:9:0,9:1:0,0:5,4\n+chrM\t15302\t\\.\tA\tG\t38\tPASS\tSAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=26.5;PSTD=1;QUAL=38;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=1;MSI=3;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=TTTACCTTTCACTTCATCTT;RSEQ=CCCTTCATTATTGCAGCCCT;DUPRATE=0;SPLITREAD=0;SPANPAIR=0\tGT:DP:VD:AD:AF:RD:ALD\t1/1:2:2:0,2:1:0,0:1,1\n+chrM\t16263\t\\.\tC\tT\t68\tPASS\tSAMPLE=Sample;TYPE=SNV;DP=4;VD=4;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=2:2;PMEAN=25.8;PSTD=1;QUAL=34.2;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=3;HIAF=1.0000;ADJAF=0;SHIFT3=4;MSI=4;MSILEN=1;NM=3.0;HICNT=3;HICOV=3;LSEQ=ACTGCAACTCCAAAGCCACC;RSEQ=CTCACCCACTAGGATACCAA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0\tGT:DP:VD:AD:AF:RD:ALD\t1/1:4:4:0,4:1:0,0:2,2\n+chrM\t16322\t\\.\tT\tC\t33\tPASS\tSAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=13.5;PSTD=1;QUAL=33.2;QSTD=1;SBF=1;ODDRATIO=0;MQ=60;SN=4;HIAF=1.0000;ADJAF=0.5;SHIFT3=0;MSI=1;MSILEN=1;NM=1.5;HICNT=2;HICOV=2;LSEQ=ACAGTACATAGTACATAAAG;RSEQ=CATTTACCGTACATAGCACA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0\tGT:DP:VD:AD:AF:RD:ALD\t1/1:2:2:0,2:1:0,0:1,1\n+chrM\t16521\t\\.\tC\tT\t38\tPASS\tSAMPLE=Sample;TYPE=SNV;DP=2;VD=2;AF=1;BIAS=0:2;REFBIAS=0:0;VARBIAS=1:1;PMEAN=33.5;PSTD=1;QUAL=38;QSTD=1;SBF=1;ODDRATIO=0;MQ=51.5;SN=4;HIAF=1.0000;ADJAF=0;SHIFT3=0;MSI=2;MSILEN=1;NM=1.0;HICNT=2;HICOV=2;LSEQ=ATCTGGTTCCTACTTCAGGG;RSEQ=CATAAAGCCTAAATAGCCCA;DUPRATE=0;SPLITREAD=0;SPANPAIR=0\tGT:DP:VD:AD:AF:RD:ALD\t1/1:2:2:0,2:1:0,0:1,1\n' |
| b |
| diff -r 5f756651a1bc -r d262577e04b0 vardict.xml --- a/vardict.xml Fri Sep 11 21:07:13 2020 +0000 +++ b/vardict.xml Tue Nov 16 19:05:56 2021 +0000 |
| [ |
| @@ -5,8 +5,8 @@ </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">vardict-java</requirement> - <requirement type="package" version="5.0.1">gawk</requirement> - <requirement type="package" version="1.10">samtools</requirement> + <requirement type="package" version="5.1.0">gawk</requirement> + <requirement type="package" version="1.14">samtools</requirement> </requirements> <expand macro="stdio" /> <command detect_errors="exit_code"><![CDATA[ @@ -86,7 +86,7 @@ <conditional name="select_mode"> <param name="mode" type="select" label="Choose run mode"> <option value="single">Single sample mode</option> - <option value="paired" selected="True">Paired variant calling</option> + <option value="paired" selected="true">Paired variant calling</option> </param> <when value="single"> <expand macro="input_default" /> @@ -96,7 +96,7 @@ <expand macro="input_default" /> </when> </conditional> - <section name="advancedsettings" title="Advanced Settings" expanded="False"> + <section name="advancedsettings" title="Advanced Settings" expanded="false"> <param argument="-f" type="float" min="0.0" max="1.0" value="0.01" label="Minimum variant allele fraction" /> <param argument="-k" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Indicate whether to perform local realignment" /> <param argument="-r" type="integer" min="0" value="2" label="Minimum number of reads supporting the variant" /> @@ -128,8 +128,8 @@ <param name="reference_source_selector" value="history"/> <param name="ref_file" ftype="fasta" value="genome.fasta" /> </conditional> - <output name="all_variants" file="all_variants_paired.vcf" /> - <output name="passed_variants" file="passed_variants_paired.vcf" /> + <output name="all_variants" compare="re_match_multiline" file="all_variants_paired.vcf" /> + <output name="passed_variants" compare="re_match_multiline" file="passed_variants_paired.vcf" /> </test> <test expect_num_outputs="2"> <conditional name="select_mode"> @@ -141,8 +141,8 @@ <param name="reference_source_selector" value="cached"/> <param name="ref_file" value="test_buildid"/> </conditional> - <output name="all_variants" file="all_variants_paired.vcf" /> - <output name="passed_variants" file="passed_variants_paired.vcf" /> + <output name="all_variants" compare="re_match_multiline" file="all_variants_paired.vcf" /> + <output name="passed_variants" compare="re_match_multiline" file="passed_variants_paired.vcf" /> </test> <test expect_num_outputs="2"> <conditional name="select_mode"> @@ -153,8 +153,8 @@ <param name="reference_source_selector" value="cached"/> <param name="ref_file" value="test_buildid"/> </conditional> - <output name="all_variants" file="all_variants_single.vcf" /> - <output name="passed_variants" file="passed_variants_single.vcf" /> + <output name="all_variants" compare="re_match_multiline" file="all_variants_single.vcf" /> + <output name="passed_variants" compare="re_match_multiline" file="passed_variants_single.vcf" /> </test> </tests> <help> |