Mercurial > repos > iuc > lofreq_filter
changeset 2:9cb929f21cfa draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"
| author | iuc |
|---|---|
| date | Sat, 21 Mar 2020 10:51:28 -0400 |
| parents | fdba1586551d |
| children | 701d134358ad |
| files | test-data/indel-call-out.vcf |
| diffstat | 1 files changed, 21 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/indel-call-out.vcf Sat Mar 21 10:51:28 2020 -0400 @@ -0,0 +1,21 @@ +##fileformat=VCFv4.0 +##fileDate=20200320 +##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/tmppZpVLj/job_working_directory/000/9/working/pp-tmp/lofreq2_call_parallele60ipsuv/0.vcf.gz reads.bam +##reference=reference.fa +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> +##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> +##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant)."> +##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position"> +#CHROM POS ID REF ALT QUAL FILTER INFO +pBR322 725 . G GN 0 . DP=46;AF=0.021739;SB=0;DP4=22,23,0,1;INDEL;HRUN=1 +pBR322 746 . A AN 0 . DP=225;AF=0.004444;SB=3;DP4=116,108,0,1;INDEL;HRUN=1 +pBR322 747 . T TN 0 . DP=230;AF=0.004348;SB=3;DP4=118,111,0,1;INDEL;HRUN=1 +pBR322 751 . G GN 0 . DP=255;AF=0.003922;SB=3;DP4=128,126,0,1;INDEL;HRUN=1 +pBR322 807 . T TN 0 . DP=606;AF=0.001650;SB=0;DP4=300,305,0,1;INDEL;HRUN=3 +pBR322 943 . C CCG 0 . DP=1465;AF=0.000683;SB=0;DP4=709,755,0,1;INDEL;HRUN=1 +pBR322 1152 . C CN 0 . DP=1754;AF=0.000570;SB=0;DP4=926,830,1,0;INDEL;HRUN=2 +pBR322 1271 . A AN 0 . DP=1743;AF=0.000574;SB=0;DP4=890,855,1,0;INDEL;HRUN=2 +pBR322 1376 . A ANN 0 . DP=1691;AF=0.000591;SB=3;DP4=849,843,0,1;INDEL;HRUN=1