Mercurial > repos > artbio > lumpy_smoove

annotate test-data/result-5.vcf @ 10:8711df965d4b draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 355389e3d1b38d93b1bc1c683c25094d5c6f8223
author artbio
date Wed, 24 Jan 2024 19:26:57 +0000
parents b4dec06d8fc6
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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1 ##fileformat=VCFv4.2
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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2 ##FILTER=<ID=PASS,Description="All filters passed">
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8711df965d4b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 355389e3d1b38d93b1bc1c683c25094d5c6f8223
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3 ##fileDate=20240124
4
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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4 ##reference=reference.fa
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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5 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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6 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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7 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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8 ##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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9 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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10 ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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11 ##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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12 ##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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13 ##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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14 ##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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15 ##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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16 ##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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17 ##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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18 ##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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19 ##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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20 ##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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21 ##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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22 ##ALT=<ID=DEL,Description="Deletion">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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23 ##ALT=<ID=DUP,Description="Duplication">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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24 ##ALT=<ID=INV,Description="Inversion">
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25 ##ALT=<ID=DUP:TANDEM,Description="Tandem duplication">
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26 ##ALT=<ID=INS,Description="Insertion of novel sequence">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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27 ##ALT=<ID=CNV,Description="Copy number variable region">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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28 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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29 ##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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30 ##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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31 ##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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32 ##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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33 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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34 ##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Phred-scaled probability that this site is variant (non-reference in this sample">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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35 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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36 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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37 ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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38 ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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39 ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of reference observations">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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40 ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of alternate observations">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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41 ##FORMAT=<ID=RS,Number=1,Type=Integer,Description="Reference allele split-read observation count, with partial observations recorded fractionally">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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42 ##FORMAT=<ID=AS,Number=A,Type=Integer,Description="Alternate allele split-read observation count, with partial observations recorded fractionally">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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43 ##FORMAT=<ID=ASC,Number=A,Type=Integer,Description="Alternate allele clipped-read observation count, with partial observations recorded fractionally">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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44 ##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Reference allele paired-end observation count, with partial observations recorded fractionally">
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45 ##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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46 ##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)">
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8711df965d4b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 355389e3d1b38d93b1bc1c683c25094d5c6f8223
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47 ##contig=<ID=chrI_sub,length=100000>
8711df965d4b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 355389e3d1b38d93b1bc1c683c25094d5c6f8223
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48 ##smoove_version=0.2.8
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49 ##smoove_count_stats=RG1:0,638,0,598
4
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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50 ##source=LUMPY
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51 ##bcftools_annotateVersion=1.17+htslib-1.17
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52 ##bcftools_annotateCommand=annotate -x INFO/PRPOS,INFO/PREND -Ou; Date=Wed Jan 24 19:28:14 2024
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49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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53 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
49da975ba395 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 83a18424ccf42793d2c7f5385b3f9ca211e49790"
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54 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
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8711df965d4b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 355389e3d1b38d93b1bc1c683c25094d5c6f8223
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55 ##bcftools_viewVersion=1.17+htslib-1.17
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56 ##bcftools_viewCommand=view -c 1 -Oz -c 1 -o output-smoove.genotyped.vcf.gz; Date=Wed Jan 24 19:28:14 2024
8711df965d4b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 355389e3d1b38d93b1bc1c683c25094d5c6f8223
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57 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT RG1
8711df965d4b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove commit 355389e3d1b38d93b1bc1c683c25094d5c6f8223
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58 chrI_sub 50000 1 N <DUP> 71.54 . SVTYPE=DUP;SVLEN=981;END=50981;STRANDS=-+:4;IMPRECISE;CIPOS=-646,29;CIEND=-30,505;CIPOS95=-164,8;CIEND95=-9,133;SU=4;PE=4;SR=0;AC=2;AN=2 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 1/1:8:71.54:-8,-2,-1:9:3:5:3:5:0:0:0:3:5:0.62