view test-data/indel-call-out.vcf @ 3:c27549b9aa1f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 0cec5f95ad0b141a9cc5be00be6d2574609b661a"

##fileformat=VCFv4.0
##fileDate=20200529
##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/lofreq2_call_parallelafbznae0/0.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	.	;HRUN=1
pBR322	746	.	A	AN	0	.	;HRUN=1
pBR322	747	.	T	TN	0	.	;HRUN=1
pBR322	751	.	G	GN	0	.	;HRUN=1
pBR322	807	.	T	TN	0	.	;HRUN=3
pBR322	943	.	C	CCG	0	.	;HRUN=1
pBR322	1152	.	C	CN	0	.	;HRUN=2
pBR322	1271	.	A	AN	0	.	;HRUN=2
pBR322	1376	.	A	ANN	0	.	;HRUN=1