Mercurial > repos > iuc > lofreq_alnqual

comparison test-data/call-out1.vcf @ 4:e0e2fd665102 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 13:13:27 -0400
parents e61c9ac190ad
children
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3:e61c9ac190ad 4:e0e2fd665102
1 ##fileformat=VCFv4.0 1 ##fileformat=VCFv4.0
2 ##fileDate=20200529 2 ##fileDate=20200615
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 3 ##source=lofreq call --verbose --ref reference.fa --sig 1 --bonf 1 --no-default-filter --no-default-filter -r pBR322:1-2180 -o /tmp/tmpe0171355/job_working_directory/000/28/working/pp-tmp/lofreq2_call_parallell2yprl2k/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">