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planemo upload for repository https://github.com/galaxyproject/tools-iuc commit c81cc2981db77f9a1a3b287d35dc7d1f13042a27
author iuc
date Wed, 25 Sep 2024 13:25:31 +0000
parents 3f6f028f418f
children 09f5c6f3088a
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##fileformat=VCFv4.2
##source=Sniffles2_2.4
##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpxu4n4sep/job_working_directory/000/4/outputs/dataset_5ee6e57f-c129-4b42-81b4-52428800dbe4.dat --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 0 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5 --allow-overwrite"
##fileDate="2024/09/14 14:15:39"
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##contig=<ID=GL000200.1,length=187035>
##contig=<ID=GL000193.1,length=189789>
##contig=<ID=GL000194.1,length=191469>
##contig=<ID=GL000225.1,length=211173>
##contig=<ID=GL000192.1,length=547496>
##contig=<ID=NC_007605,length=171823>
##contig=<ID=hs37d5,length=35477943>
##ALT=<ID=INS,Description="Insertion">
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=DUP,Description="Duplication">
##ALT=<ID=INV,Description="Inversion">
##ALT=<ID=BND,Description="Breakend; Translocation">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
##FORMAT=<ID=DR,Number=1,Type=Integer,Description="Number of reference reads">
##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of variant reads">
##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phase-block, zero if none or not phased">
##FORMAT=<ID=ID,Number=1,Type=String,Description="Individual sample SV ID for multi-sample output">
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=GT,Description="Genotype filter">
##FILTER=<ID=SUPPORT_MIN,Description="Minimum read support filter">
##FILTER=<ID=STDEV_POS,Description="SV Breakpoint standard deviation filter">
##FILTER=<ID=STDEV_LEN,Description="SV length standard deviation filter">
##FILTER=<ID=COV_MIN,Description="Minimum coverage filter">
##FILTER=<ID=COV_MIN_GT,Description="Minimum coverage filter (missing genotype)">
##FILTER=<ID=COV_CHANGE,Description="Coverage change filter">
##FILTER=<ID=COV_CHANGE_INS,Description="Coverage change filter for INS">
##FILTER=<ID=COV_CHANGE_FRAC_US,Description="Coverage fractional change filter: upstream-start">
##FILTER=<ID=COV_CHANGE_FRAC_SC,Description="Coverage fractional change filter: start-center">
##FILTER=<ID=COV_CHANGE_FRAC_CE,Description="Coverage fractional change filter: center-end">
##FILTER=<ID=COV_CHANGE_FRAC_ED,Description="Coverage fractional change filter: end-downstream">
##FILTER=<ID=MOSAIC_AF,Description="Mosaic variant allele frequency filter">
##FILTER=<ID=NOT_MOSAIC_AF,Description="Variant allele frequency filter for non-mosaic">
##FILTER=<ID=ALN_NM,Description="Length adjusted mismatch filter">
##FILTER=<ID=STRAND_BND,Description="Strand support filter for BNDs">
##FILTER=<ID=STRAND,Description="Strand support filter for germline SVs">
##FILTER=<ID=STRAND_MOSAIC,Description="Strand support filter for mosaic SVs">
##FILTER=<ID=SVLEN_MIN,Description="SV length filter">
##FILTER=<ID=SVLEN_MIN_MOSAIC,Description="SV length filter for mosaic SVs">
##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Structural variation with precise breakpoints">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Structural variation with imprecise breakpoints">
##INFO=<ID=MOSAIC,Number=0,Type=Flag,Description="Structural variation classified as putative mosaic">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of structural variation">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variation">
##INFO=<ID=CHR2,Number=1,Type=String,Description="Mate chromsome for BND SVs">
##INFO=<ID=SUPPORT,Number=1,Type=Integer,Description="Number of reads supporting the structural variation">
##INFO=<ID=SUPPORT_INLINE,Number=1,Type=Integer,Description="Number of reads supporting an INS/DEL SV (non-split events only)">
##INFO=<ID=SUPPORT_LONG,Number=1,Type=Integer,Description="Number of soft-clipped reads putatively supporting the long insertion SV">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of structural variation">
##INFO=<ID=STDEV_POS,Number=1,Type=Float,Description="Standard deviation of structural variation start position">
##INFO=<ID=STDEV_LEN,Number=1,Type=Float,Description="Standard deviation of structural variation length">
##INFO=<ID=COVERAGE,Number=.,Type=Float,Description="Coverages near upstream, start, center, end, downstream of structural variation">
##INFO=<ID=STRAND,Number=1,Type=String,Description="Strands of supporting reads for structural variant">
##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count, summed up over all samples">
##INFO=<ID=SUPP_VEC,Number=1,Type=String,Description="List of read support for all samples">
##INFO=<ID=CONSENSUS_SUPPORT,Number=1,Type=Integer,Description="Number of reads that support the generated insertion (INS) consensus sequence">
##INFO=<ID=RNAMES,Number=.,Type=String,Description="Names of supporting reads (if enabled with --output-rnames)">
##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
##INFO=<ID=NM,Number=.,Type=Float,Description="Mean number of query alignment length adjusted mismatches of supporting reads">
##INFO=<ID=PHASE,Number=.,Type=String,Description="Phasing information derived from supporting reads, represented as list of: HAPLOTYPE,PHASESET,HAPLOTYPE_SUPPORT,PHASESET_SUPPORT,HAPLOTYPE_FILTER,PHASESET_FILTER">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE
21	21492142	Sniffles2.DEL.0S14	N	<DEL>	52	PASS	PRECISE;SVTYPE=DEL;SVLEN=-506;END=21492648;SUPPORT=48;COVERAGE=46,43,43,43,48;STRAND=+-;AF=1.000;STDEV_LEN=0.509;STDEV_POS=1.404	GT:GQ:DR:DV	1/1:60:0:48