Mercurial > repos > iuc > lofreq_indelqual

comparison test-data/indel-call-out.vcf @ 4:354b534eeab7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 841c48994eb214a2f8718b1d1aca22bc38598528"
author iuc
date Mon, 15 Jun 2020 13:12:40 -0400
parents c27549b9aa1f
children
comparison
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3:c27549b9aa1f 4:354b534eeab7
1 ##fileformat=VCFv4.0 1 ##fileformat=VCFv4.0
2 ##fileDate=20200529 2 ##fileDate=20200615
3 ##source=lofreq call --verbose --ref reference.fa --call-indels --only-indels --sig 1 --bonf 1 --no-default-filter --no-default-filter -r pBR322:1-2180 -o /tmp/lofreq2_call_parallelafbznae0/0.vcf.gz reads.bam 3 ##source=lofreq call --verbose --ref reference.fa --call-indels --only-indels --sig 1 --bonf 1 --no-default-filter --no-default-filter -r pBR322:1-2180 -o /tmp/tmp265htsdc/job_working_directory/000/31/working/pp-tmp/lofreq2_call_parallel4gfado3q/0.vcf.gz reads.bam
4 ##reference=reference.fa 4 ##reference=reference.fa
5 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> 5 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
6 ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> 6 ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
7 ##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position"> 7 ##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
8 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> 8 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
9 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 9 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
10 ##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant)."> 10 ##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
11 ##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position"> 11 ##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
12 #CHROM POS ID REF ALT QUAL FILTER INFO 12 #CHROM POS ID REF ALT QUAL FILTER INFO
13 pBR322 725 . G GN 0 . ;HRUN=1 13 pBR322 725 . G GN 0 . DP=46;AF=0.021739;SB=0;DP4=22,23,0,1;INDEL;HRUN=1
14 pBR322 746 . A AN 0 . ;HRUN=1 14 pBR322 746 . A AN 0 . DP=225;AF=0.004444;SB=3;DP4=116,108,0,1;INDEL;HRUN=1
15 pBR322 747 . T TN 0 . ;HRUN=1 15 pBR322 747 . T TN 0 . DP=230;AF=0.004348;SB=3;DP4=118,111,0,1;INDEL;HRUN=1
16 pBR322 751 . G GN 0 . ;HRUN=1 16 pBR322 751 . G GN 0 . DP=255;AF=0.003922;SB=3;DP4=128,126,0,1;INDEL;HRUN=1
17 pBR322 807 . T TN 0 . ;HRUN=3 17 pBR322 807 . T TN 0 . DP=606;AF=0.001650;SB=0;DP4=300,305,0,1;INDEL;HRUN=3
18 pBR322 943 . C CCG 0 . ;HRUN=1 18 pBR322 943 . C CCG 0 . DP=1465;AF=0.000683;SB=0;DP4=709,755,0,1;INDEL;HRUN=1
19 pBR322 1152 . C CN 0 . ;HRUN=2 19 pBR322 1152 . C CN 0 . DP=1754;AF=0.000570;SB=0;DP4=926,830,1,0;INDEL;HRUN=2
20 pBR322 1271 . A AN 0 . ;HRUN=2 20 pBR322 1271 . A AN 0 . DP=1743;AF=0.000574;SB=0;DP4=890,855,1,0;INDEL;HRUN=2
21 pBR322 1376 . A ANN 0 . ;HRUN=1 21 pBR322 1376 . A ANN 0 . DP=1691;AF=0.000591;SB=3;DP4=849,843,0,1;INDEL;HRUN=1