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view test-data/call-out2.vcf @ 5:65432c3abf6c 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 13:13:03 -0400
parents 074d44697036
children
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##fileformat=VCFv4.0
##fileDate=20200615
##source=lofreq call --verbose --ref reference.fa --sig 1 --bonf 1 --no-default-filter --no-default-filter -r pBR322:1-2180 -o /tmp/tmp265htsdc/job_working_directory/000/28/working/pp-tmp/lofreq2_call_parallelg3dmyvln/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	815	.	A	G	0	.	DP=665;AF=0.003008;SB=6;DP4=333,311,0,2
pBR322	861	.	A	C	0	.	DP=946;AF=0.002114;SB=3;DP4=447,497,0,2
pBR322	1001	.	A	C	0	.	DP=1797;AF=0.000556;SB=3;DP4=877,918,1,0
pBR322	1013	.	C	G	0	.	DP=1773;AF=0.000564;SB=0;DP4=875,897,0,1
pBR322	1068	.	T	G	0	.	DP=1774;AF=0.000564;SB=3;DP4=853,920,1,0
pBR322	1084	.	G	T	0	.	DP=1789;AF=0.000559;SB=3;DP4=875,913,1,0
pBR322	1113	.	T	A	0	.	DP=1784;AF=0.000561;SB=0;DP4=885,898,0,1
pBR322	1134	.	C	T	49314	.	DP=1767;AF=1.000000;SB=0;DP4=0,0,910,857
pBR322	1193	.	G	A	0	.	DP=1698;AF=0.000589;SB=3;DP4=865,832,0,1
pBR322	1218	.	A	C	0	.	DP=1708;AF=0.000585;SB=3;DP4=875,831,0,1
pBR322	1230	.	T	C	0	.	DP=1759;AF=0.000569;SB=3;DP4=907,850,0,1
pBR322	1256	.	A	G	0	.	DP=1746;AF=0.000573;SB=0;DP4=902,842,1,0
pBR322	1498	.	C	G	0	.	DP=1195;AF=0.000837;SB=3;DP4=588,606,1,0
pBR322	1503	.	T	G	0	.	DP=1156;AF=0.000865;SB=3;DP4=563,592,1,0
pBR322	1505	.	G	A	0	.	DP=1137;AF=0.000880;SB=0;DP4=560,576,0,1