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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit c1fda24943cf04866d408133ffb6aabf4a90866b"
author iuc
date Mon, 05 Oct 2020 20:15:16 +0000
parents af7e416d8176
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##fileformat=VCFv4.0
##fileDate=20200615
##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 
##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