| Previous changeset 0:2975b29bcaa1 (2020-08-25) Next changeset 2:d262577e04b0 (2021-11-16) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 2690164244722cfc32811015f2408b8275f06378" |
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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 |
| b |
| diff -r 2975b29bcaa1 -r 5f756651a1bc macros.xml --- a/macros.xml Tue Aug 25 05:41:19 2020 -0400 +++ b/macros.xml Fri Sep 11 21:07:13 2020 +0000 |
| b |
| @@ -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)" /> |
| b |
| diff -r 2975b29bcaa1 -r 5f756651a1bc test-data/all_variants_paired.vcf --- 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 |
| b |
| b'@@ -1,10 +1,11 @@\n-##fileformat=VCFv4.1\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=1,Type=Float,Description="Allele Frequency">\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@@ -13,6 +14,8 @@\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@@ -25,8 +28,6 @@\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=P0.01Likely,Description="Likely candidate but p-value > 0.01/5**vd2">\n-##FILTER=<ID=InDelLikely,Description="Likely Indels are not considered somatic">\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@@ -39,67 +40,67 @@\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=1,Type=Float,Description="Allele Frequency">\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=1,Type=String,Description="Strand Bias Info">\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,Number=1,Type=Float,Description="Strand Bias Odds ratio">\n-##FORMAT=<ID=MQ,Number=1,Type=Float,Description="Mean Mapping Quality">\n+##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="Mean Mapping Quality">\n ##FORMAT=<ID=SN,Number=1,Type=Float,Description="Signal to noise">\n ##FORMAT=<ID=HIAF,Number=1,Type=Float,Description="Allele frequency using only high quality bases">\n ##FORMAT=<ID=NM,Number=1,Type=Float,Description="Mean mismatches in reads">\n #CHROM\tPOS\tID\tREF\tALT\t'..b';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\t15933\t.\tC\tT\t57\td5;v3;f0.01;p8;pSTD;q22.5;Q0;SN1.5\tSTATUS=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\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@@ -108,4 +109,4 @@\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\t1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:38:1:1:0:51.5:4:1:0:1\t1/1:11:11:5,6:0,0:0,11:1:0,2:20.8:1:32.9:1:1:0:49.6:2.667:1:0.0909:1\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 2975b29bcaa1 -r 5f756651a1bc test-data/all_variants_single.vcf --- 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 |
| b |
| @@ -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"> |
| b |
| diff -r 2975b29bcaa1 -r 5f756651a1bc test-data/passed_variants_paired.vcf --- 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 |
| b |
| b'@@ -1,10 +1,11 @@\n-##fileformat=VCFv4.1\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=1,Type=Float,Description="Allele Frequency">\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@@ -13,6 +14,8 @@\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@@ -25,8 +28,6 @@\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=P0.01Likely,Description="Likely candidate but p-value > 0.01/5**vd2">\n-##FILTER=<ID=InDelLikely,Description="Likely Indels are not considered somatic">\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@@ -39,49 +40,49 @@\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=1,Type=Float,Description="Allele Frequency">\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=1,Type=String,Description="Strand Bias Info">\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,Number=1,Type=Float,Description="Strand Bias Odds ratio">\n-##FORMAT=<ID=MQ,Number=1,Type=Float,Description="Mean Mapping Quality">\n+##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="Mean Mapping Quality">\n ##FORMAT=<ID=SN,Number=1,Type=Float,Description="Signal to noise">\n ##FORMAT=<ID=HIAF,Number=1,Type=Float,Description="Allele frequency using only high quality bases">\n ##FORMAT=<ID=NM,Number=1,Type=Float,Description="Mean mismatches in reads">\n #CHROM\tPOS\tID\tREF\tALT\t'..b'F=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\t0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0\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\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@@ -89,4 +90,4 @@\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\t1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:38:1:1:0:51.5:4:1:0:1\t1/1:11:11:5,6:0,0:0,11:1:0,2:20.8:1:32.9:1:1:0:49.6:2.667:1:0.0909:1\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 2975b29bcaa1 -r 5f756651a1bc test-data/passed_variants_single.vcf --- 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 |
| b |
| @@ -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"> |
| b |
| diff -r 2975b29bcaa1 -r 5f756651a1bc vardict.xml --- 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 && |