Mercurial > repos > iuc > lofreq_call

comparison test-data/call-out1.vcf @ 4:074d44697036 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 0cec5f95ad0b141a9cc5be00be6d2574609b661a"
author iuc
date Fri, 29 May 2020 15:23:20 -0400
parents 31216d510164
children 65432c3abf6c
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3:3b4b2121842f 4:074d44697036
1 ##fileformat=VCFv4.0 1 ##fileformat=VCFv4.0
2 ##fileDate=20191125 2 ##fileDate=20200529
3 ##source=lofreq call --verbose --ref reference.fa --sig 0.01 --bonf dynamic --no-default-filter -r pBR322:1-2180 -o /tmp/lofreq2_call_parallel3mrmthi_/0.vcf.gz alignments.bam 3 ##source=lofreq call --verbose --ref reference.fa --min-cov 1 --max-depth 1000000 --min-bq 6 --min-alt-bq 6 --min-mq 0 --max-mq 255 --src-qual --ign-vcf ign0.vcf --def-nm-q 40 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic --no-default-filter -r pBR322:1-2180 -o /tmp/lofreq2_call_parallelqgn6kxdr/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">