view test-data/call-out1.vcf @ 6:971e07ca4456 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3751719cd03b8380954e2231cf91496c863056e2

##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/tmpe0171355/job_working_directory/000/28/working/pp-tmp/lofreq2_call_parallell2yprl2k/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">
##FILTER=<ID=min_snvqual_38,Description="Minimum SNV Quality (Phred) 38">
##FILTER=<ID=min_indelqual_20,Description="Minimum Indel Quality (Phred) 20">
##FILTER=<ID=min_dp_10,Description="Minimum Coverage 10">
##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
##FILTER=<ID=min_snvqual_38,Description="Minimum SNV Quality (Phred) 38">
##FILTER=<ID=min_indelqual_20,Description="Minimum Indel Quality (Phred) 20">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
pBR322	1134	.	C	T	49314	PASS	DP=1767;AF=1.000000;SB=0;DP4=0,0,910,857