| Next changeset 1:5f756651a1bc (2020-09-11) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 8a561c35737f2bdef39842ce7f297a286380bf36" |
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added:
macros.xml test-data/all_variants_paired.vcf test-data/all_variants_single.vcf test-data/fasta_indexes.loc test-data/genome.fasta test-data/genome.fasta.fai test-data/normal.bam test-data/passed_variants_paired.vcf test-data/passed_variants_single.vcf test-data/tumor.bam tool-data/fasta_indexes.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test vardict.xml |
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| diff -r 000000000000 -r 2975b29bcaa1 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Aug 25 05:41:19 2020 -0400 |
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| @@ -0,0 +1,24 @@ +<macros> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@TOOL_VERSION@">1.7.0</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="history">Use a genome from the history</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Reference Genome File"> + <options from_data_table="fasta_indexes"/> + </param> + </when> + <when value="history"> + <param name="ref_file" format="fasta" type="data" label="Reference Genome File" /> + </when> + </conditional> + </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)" /> + </xml> +</macros> |
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| diff -r 000000000000 -r 2975b29bcaa1 test-data/all_variants_paired.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_variants_paired.vcf Tue Aug 25 05:41:19 2020 -0400 |
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| b'@@ -0,0 +1,111 @@\n+##fileformat=VCFv4.1\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=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+##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=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+##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=1,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=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=SN,Number=1,Type=Float,Description="Signal to nois'..b'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\t0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0\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\t0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0\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\t1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:38:1:1:0:51.5:4:1:0:1\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' 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| diff -r 000000000000 -r 2975b29bcaa1 test-data/all_variants_single.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_variants_single.vcf Tue Aug 25 05:41:19 2020 -0400 |
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| b'@@ -0,0 +1,91 @@\n+##fileformat=VCFv4.1\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 within 0 bp">\n+##FILTER=<ID='..b'ITREAD=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\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 000000000000 -r 2975b29bcaa1 test-data/fasta_indexes.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_indexes.loc Tue Aug 25 05:41:19 2020 -0400 |
| b |
| @@ -0,0 +1,26 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +test_buildid hg17 test_displayname ${__HERE__}/genome.fasta |
| b |
| diff -r 000000000000 -r 2975b29bcaa1 test-data/genome.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome.fasta Tue Aug 25 05:41:19 2020 -0400 |
| b |
| b'@@ -0,0 +1,333 @@\n+>chrM\n+NNNCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT\n+TTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTG\n+GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATT\n+CTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACCTACTA\n+AAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAAT\n+GTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA\n+AACCCCCCCCTCCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGC\n+CAAACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAAT\n+TTTATCTTTAGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACA\n+TTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATACAACCCCC\n+GCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAAC\n+CAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCA\n+AAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAA\n+ATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGC\n+AAGCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAG\n+GGACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCC\n+ACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGT\n+TTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACC\n+GCGGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTT\n+TAGATCACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAA\n+CTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAAC\n+ACACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGC\n+CCTAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAGAACACTACGA\n+GCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGA\n+GGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGC\n+TCAGCCTATATACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGT\n+AAGCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGG\n+TGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTT\n+ATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTGAGAGTAGAGT\n+GCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCC\n+TCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATA\n+GAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACG\n+AACCAGAGTGTAGCTTAACACAAAGCACCCAACTTACACTTAGGAGATTT\n+CAACTTAACTTGACCGCTCTGAGCTAAACCTAGCCCCAAACCCACTCCAC\n+CTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGG\n+CGATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGA\n+TGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTT\n+CTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAA\n+GACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCC\n+GTCTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCT\n+ACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTTAGTTCAACTT\n+TAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAG\n+TCCAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGA\n+GTAAAAAATTTAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGA\n+AAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAACATATAACT\n+GAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAA\n+TGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCA\n+GATCAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCA\n+ACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAG\n+GAAAGGTTAAAAAAAGTAAAAGGAACTCGGCAAACCTTACCCCGCCTGTT\n+TACCAAAAACATCACCTCTAGCATCACCAGTATTAGAGGCACCGCCTGCC\n+CAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAaaggtagca\n+taatcacttgttccttaaatagggacctgtatgaatggctccacgagggt\n+tcagctgtctcttacttttaaccagtgaaattgacctgcccgtgaagagg\n+cgggcatgacacagcaagacgagaagaccctatggagctttaatttaTTA\n+ATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCA\n+TTAAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCA\n+GTACATGCTAAGACTTCACCAGTCAAAGCGAACTACTATACTCAATTGAT\n+CCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATC\n+CTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGAT\n+CAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGA\n+TTAAAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTT\n+CTATCTACTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCC\n+TACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTAT\n+TATACCCACACCCACCCAAGAACAGGGTTTgttaagatggcagagcccgg\n+taatcgcataaaacttaaaactttacagtcagaggttcaattcctcttct\n+taacaacaTACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAA\n+TCGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATA\n+CAACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCTACTACAACC\n+CTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCA\n+CATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATC\n+GCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCT\n+CAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACT\n+CAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGC\n+GCACTGCGAGCAGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCAT\n+CATTCTACTATCAACATTACTAATAAGTGGCTCCTTTAACCTCTCCACCC\n+TTATCACAACACAAGAACACC'..b'TTAGTTACCGCTAACAACCTATT\n+CCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCA\n+TCAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCA\n+GTCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCATG\n+ATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAA\n+ACGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCA\n+GGCAAATCAGCCCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGA\n+AGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTATAGTTGTAG\n+CAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCA\n+CTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGC\n+AGCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCT\n+CCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAA\n+CCACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCAT\n+ACTATTTATGTGCTCCGGGTCCATCATCCACAACCTTAACAATGAACAAG\n+ATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTCACTTCAACC\n+TCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGG\n+TTTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAA\n+ACGCCTGAGCCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCC\n+TATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCC\n+CACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTA\n+AACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCATTACTAACAAC\n+ATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAACT\n+CACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCA\n+ACTACCTAACCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTAT\n+TTCTCCAACATACTCGGATTCTACCCTAGCATCACACACCGCACAATCCC\n+CTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACC\n+TAACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATC\n+TCCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACTT\n+CCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAAC\n+CTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGT\n+TCAACCAGTAACCACTACTAATCAACGCCCATAATCATACAAAGCCCCCG\n+CACCAATAGGATCCTCCCGAATCAACCCTGACCCCTCTCCTTCATAAATT\n+ATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATA\n+CTCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAA\n+CACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCA\n+ATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATA\n+AATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAA\n+TAACACACCCGACCACACCGCTAACAATCAGTACTAAACCCCCATAAATA\n+GGAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTAAACCCACACT\n+CAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGA\n+CCAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATG\n+ACCCCAATACGCAAAATTAACCCCCTAATAAAATTAATTAACCACTCATT\n+CATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAAACTTCGGCT\n+CACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTA\n+GCCATACACTACTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCA\n+CATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCCA\n+ATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGC\n+CTATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTAT\n+CCTCCTGCTTGCAACTATAGCAACAGCCTTCATAGGCTATGTCCTCCCGT\n+GAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAACTTACTATCC\n+GCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTA\n+CTCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCT\n+TACCCTTCATTATTGCAGCCCTAGCAGCACTCCACCTCCTATTCTTGCAC\n+GAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAAT\n+CACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCT\n+TCCTTCTCTCCTTAATGACATTAACACTATTCTCACCAGACCTCCTAGGC\n+GACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCCTCCCCACAT\n+CAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCC\n+CTAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTA\n+GCAATAATCCCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCG\n+CCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTC\n+TAACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGA\n+CAAGTAGCATCCGTACTATACTTCACAACAATCCTAATCCTAATACCAAC\n+TATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGTA\n+TAAACTAATACACCAGTCTTGTAAACCGGAGACGAAAACCTTTTTCCAAG\n+GACAAATCAGAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAA\n+GATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGG\n+TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC\n+ATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCA\n+CCTGTAGTACATAAAAACCCAACCCACATCAAACCCCCCCCCCCCATGCT\n+TACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAAC\n+TCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTT\n+AACAGTACATAGTACATAAAGTCATTTACCGTACATAGCACATTACAGTC\n+AAATCCCTTCTCGTCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTG\n+ACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCT\n+CGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGAC\n+ATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCC\n+CTTAAATAAGACATCACGATG\n' |
| b |
| diff -r 000000000000 -r 2975b29bcaa1 test-data/genome.fasta.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome.fasta.fai Tue Aug 25 05:41:19 2020 -0400 |
| b |
| @@ -0,0 +1,1 @@ +chrM 16571 6 50 51 |
| b |
| diff -r 000000000000 -r 2975b29bcaa1 test-data/normal.bam |
| b |
| Binary file test-data/normal.bam has changed |
| b |
| diff -r 000000000000 -r 2975b29bcaa1 test-data/passed_variants_paired.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/passed_variants_paired.vcf Tue Aug 25 05:41:19 2020 -0400 |
| b |
| b'@@ -0,0 +1,92 @@\n+##fileformat=VCFv4.1\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=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+##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=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+##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=1,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=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=SN,Number=1,Type=Float,Description="Signal to noise'..b'SILEN=1;SSF=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\t0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0\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\t0/0:0:0:0,0:0,0:0,0:0:0:0:0:0:0:1:0:0:0:0:0:0\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\t1/1:2:2:1,1:0,0:0,2:1:0,2:33.5:1:38:1:1:0:51.5:4:1:0:1\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' |
| b |
| diff -r 000000000000 -r 2975b29bcaa1 test-data/passed_variants_single.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/passed_variants_single.vcf Tue Aug 25 05:41:19 2020 -0400 |
| b |
| b'@@ -0,0 +1,89 @@\n+##fileformat=VCFv4.1\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 within 0 bp">\n+##FILTER=<ID='..b'0;SPANPAIR=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' |
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| diff -r 000000000000 -r 2975b29bcaa1 test-data/tumor.bam |
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| Binary file test-data/tumor.bam has changed |
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| diff -r 000000000000 -r 2975b29bcaa1 tool-data/fasta_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Tue Aug 25 05:41:19 2020 -0400 |
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| @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa |
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| diff -r 000000000000 -r 2975b29bcaa1 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Aug 25 05:41:19 2020 -0400 |
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| @@ -0,0 +1,6 @@ +<tables> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc"/> + </table> +</tables> |
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| diff -r 000000000000 -r 2975b29bcaa1 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue Aug 25 05:41:19 2020 -0400 |
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| @@ -0,0 +1,7 @@ +<tables> + <!-- Location of SAMTools indexed FASTA files --> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/fasta_indexes.loc" /> + </table> +</tables> |
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| diff -r 000000000000 -r 2975b29bcaa1 vardict.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vardict.xml Tue Aug 25 05:41:19 2020 -0400 |
| [ |
| b'@@ -0,0 +1,176 @@\n+<tool id="vardict_java" name="VarDict" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n+ <description>calls SNVs and indels for tumor-normal pairs</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">vardict-java</requirement>\n+ <requirement type="package" version="5.0.1">gawk</requirement>\n+ <requirement type="package" version="1.10">samtools</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ #if $select_mode.mode == "paired"\n+ ln -s \'$select_mode.normal\' ./normal.bam &&\n+ ln -s \'$select_mode.normal.metadata.bam_index\' ./normal.bam.bai &&\n+ #end if\n+ ln -s \'$select_mode.tumor\' ./tumor.bam &&\n+ ln -s \'$select_mode.tumor.metadata.bam_index\' ./tumor.bam.bai &&\n+\n+ ## INDEX REFERENCE FASTA FILE IF FROM HISTORY\n+ #if $reference_source.reference_source_selector == "history":\n+ ln -s \'$reference_source.ref_file\' ./ref.fa &&\n+ samtools faidx ./ref.fa 2>&1 || echo \'Error running samtools faidx for indexing fasta reference for vardict\' >&2 &&\n+ #else if $reference_source.reference_source_selector == "cached"\n+ ln -s \'$reference_source.ref_file.fields.path\' ./ref.fa &&\n+ ln -s \'${reference_source.ref_file.fields.path}.fai\' ./ref.fa.fai &&\n+ #end if\n+\n+ ## build BED file from chromosome list\n+ #if $interval_file:\n+ grep -w -f \'$interval_file\' ./ref.fa.fai > ./chromosomes.fa.fai &&\n+ #else\n+ ln -s ./ref.fa.fai ./chromosomes.fa.fai &&\n+ #end if\n+ awk \'BEGIN {FS=OFS="\\t"} {print $1, "1", $2}\' ./chromosomes.fa.fai > ./regions.bed &&\n+\n+ vardict-java\n+ #if $select_mode.mode == "paired"\n+ -b "./tumor.bam|./normal.bam"\n+ -N \'Tumor\'\n+ #else\n+ -b "./tumor.bam"\n+ -N \'Sample\'\n+ #end if\n+ -G ./ref.fa\n+ -z\n+ -th \\${GALAXY_SLOTS:-1}\n+\n+ -f \'$advancedsettings.f\'\n+ -k \'$advancedsettings.k\'\n+ -r \'$advancedsettings.r\'\n+ -B \'$advancedsettings.B\'\n+ -Q \'$advancedsettings.Q\'\n+ -q \'$advancedsettings.q\'\n+ -m \'$advancedsettings.m\'\n+ -T \'$advancedsettings.T\'\n+ -X \'$advancedsettings.X\'\n+ -P \'$advancedsettings.P\'\n+ -o \'$advancedsettings.o\'\n+ -O \'$advancedsettings.O\'\n+ -V \'$advancedsettings.V\'\n+\n+ ## construct VFC table\n+ -c 1 -S 2 -E 3 -g 4\n+ ./regions.bed\n+\n+ ## postprocessing\n+ #if $select_mode.mode == "paired"\n+ | testsomatic.R\n+ | var2vcf_paired.pl\n+ -N \'Tumor|Normal\'\n+ #else\n+ | teststrandbias.R\n+ | var2vcf_valid.pl\n+ -N \'Sample\'\n+ -E\n+ #end if\n+ -f \'$advancedsettings.f\'\n+\n+ > \'$all_variants\' &&\n+\n+ ## Filter for PASS variants\n+ awk \'BEGIN {FS=OFS="\\t"} substr(\\$0, 1, 1) == "#" {print \\$0; next} \\$7 == "PASS" {print \\$0}\' \'$all_variants\' > \'$passed_variants\'\n+ ]]></command>\n+ <inputs>\n+ <conditional name="select_mode">\n+ <param name="mode" type="select" label="Choose run mode">\n+ <option value="single">Single sample mode</option>\n+ <option value="paired" selected="True">Paired variant calling</option>\n+ </param>\n+ <when value="single">\n+ <expand macro="input_default" />\n+ </when>\n+ <when value="paired">\n+ <param name="normal" type="data" format="bam" label="Normal file" />\n+ <expand macro="input_default" />\n+ </when>\n+ </conditional>\n+ <section name="advancedsettings" title="Advanced Settings" expanded="False">\n+ <param argument="-f" type="float" min="0.0" max="1.0" value="0.01" label="Minimum var'..b' argument="-T" type="integer" value="0" label="Maximum number of bases considered from 5\' end (default: 0, no trimming)" />\n+ <param argument="-X" type="integer" value="3" label="Maximum number of extended based after indel to look for mismatches" />\n+ <param argument="-P" type="integer" value="5" label="Maximum average read position for a variant to be considered." />\n+ <param argument="-q" type="integer" value="25" label="Minimum phred score for a base to be considered a good call" />\n+ <param argument="-o" type="float" value="1.5" label="Minimum quality ratio [(good_quality_reads)/(bad_quality_reads+0.5)] (based on definition of a good call; see previous option)" />\n+ <param argument="-O" type="float" min="0" value="0" label="Minimum average mapping quality" />\n+ <param argument="-V" type="float" min="0.0" max="1.0" value="0.05" label="Maximum allowed variant allele fraction in the normal sample" />\n+ </section>\n+ <expand macro="ref_select" />\n+ </inputs>\n+ <outputs>\n+ <data name="all_variants" format="vcf" label="VarDict SNVs and Indels (All)" />\n+ <data name="passed_variants" format="vcf" label="VarDict SNVs and Indels (Passed)" />\n+ </outputs>\n+ <tests>\n+ <test expect_num_outputs="2">\n+ <conditional name="select_mode">\n+ <param name="mode" value="paired" />\n+ <param name="normal" ftype="bam" value="normal.bam" />\n+ <param name="tumor" ftype="bam" value="tumor.bam" />\n+ </conditional>\n+ <conditional name="reference_source">\n+ <param name="reference_source_selector" value="history"/>\n+ <param name="ref_file" ftype="fasta" value="genome.fasta" />\n+ </conditional>\n+ <output name="all_variants" file="all_variants_paired.vcf" />\n+ <output name="passed_variants" file="passed_variants_paired.vcf" />\n+ </test>\n+ <test expect_num_outputs="2">\n+ <conditional name="select_mode">\n+ <param name="mode" value="paired" />\n+ <param name="normal" ftype="bam" value="normal.bam" />\n+ <param name="tumor" ftype="bam" value="tumor.bam" />\n+ </conditional>\n+ <conditional name="reference_source">\n+ <param name="reference_source_selector" value="cached"/>\n+ <param name="ref_file" value="test_buildid"/>\n+ </conditional>\n+ <output name="all_variants" file="all_variants_paired.vcf" />\n+ <output name="passed_variants" file="passed_variants_paired.vcf" />\n+ </test>\n+ <test expect_num_outputs="2">\n+ <conditional name="select_mode">\n+ <param name="mode" value="single" />\n+ <param name="tumor" ftype="bam" value="tumor.bam" />\n+ </conditional>\n+ <conditional name="reference_source">\n+ <param name="reference_source_selector" value="cached"/>\n+ <param name="ref_file" value="test_buildid"/>\n+ </conditional>\n+ <output name="all_variants" file="all_variants_single.vcf" />\n+ <output name="passed_variants" file="passed_variants_single.vcf" />\n+ </test>\n+ </tests>\n+ <help>\n+ <![CDATA[\n+VarDict\n+=======\n+\n+VarDict is a sensitive variant caller for both single and paired sample variant calling from BAM files.\n+VarDict implements several novel features such as amplicon bias aware variant calling from targeted sequencing experiments,\n+rescue of long indels by realigning bwa soft clipped reads and better scalability than many other Java based variant callers.\n+\n+For more information see the VarDict documentation_.\n+\n+.. _documentation: https://github.com/AstraZeneca-NGS/VarDictJava\n+ ]]>\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1093/nar/gkw227</citation>\n+ </citations>\n+</tool>\n' |