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comparison test-data/expected_outcome6.vcf @ 5:ceff2f6a5368 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc commit a2dd716a67d60533534269faef8e87e30496bce0
author iuc
date Thu, 14 Nov 2024 07:25:22 +0000
parents 43fffeed243f
children
comparison
equal deleted inserted replaced
4:43fffeed243f 5:ceff2f6a5368
1 ##fileformat=VCFv4.2 1 ##fileformat=VCFv4.2
2 ##source=Sniffles2_2.4 2 ##source=Sniffles2_2.5
3 ##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpbu008nw6/job_working_directory/000/13/outputs/dataset_93c07e69-9ce4-4394-84c8-8a51cb2e2c89.dat --allow-overwrite --reference reference.fa --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5" 3 ##command="/home/ross/miniconda3/envs/__sniffles@2.5.2/bin/sniffles -t 1 -i input.bam -v /tmp/tmpqwecq14c/job_working_directory/000/13/outputs/dataset_46e2d702-73e3-453f-9f8c-fba7467d34a7.dat --allow-overwrite --reference reference.fa --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5"
4 ##fileDate="2024/09/28 23:21:51" 4 ##fileDate="2024/11/13 10:05:40"
5 ##contig=<ID=1,length=249250621> 5 ##contig=<ID=1,length=249250621>
6 ##contig=<ID=2,length=243199373> 6 ##contig=<ID=2,length=243199373>
7 ##contig=<ID=3,length=198022430> 7 ##contig=<ID=3,length=198022430>
8 ##contig=<ID=4,length=191154276> 8 ##contig=<ID=4,length=191154276>
9 ##contig=<ID=5,length=180915260> 9 ##contig=<ID=5,length=180915260>
104 ##FILTER=<ID=SUPPORT_MIN,Description="Minimum read support filter"> 104 ##FILTER=<ID=SUPPORT_MIN,Description="Minimum read support filter">
105 ##FILTER=<ID=STDEV_POS,Description="SV Breakpoint standard deviation filter"> 105 ##FILTER=<ID=STDEV_POS,Description="SV Breakpoint standard deviation filter">
106 ##FILTER=<ID=STDEV_LEN,Description="SV length standard deviation filter"> 106 ##FILTER=<ID=STDEV_LEN,Description="SV length standard deviation filter">
107 ##FILTER=<ID=COV_MIN,Description="Minimum coverage filter"> 107 ##FILTER=<ID=COV_MIN,Description="Minimum coverage filter">
108 ##FILTER=<ID=COV_MIN_GT,Description="Minimum coverage filter (missing genotype)"> 108 ##FILTER=<ID=COV_MIN_GT,Description="Minimum coverage filter (missing genotype)">
109 ##FILTER=<ID=COV_CHANGE,Description="Coverage change filter"> 109 ##FILTER=<ID=COV_CHANGE_DEL,Description="Coverage change filter for DEL">
110 ##FILTER=<ID=COV_CHANGE_DUP,Description="Coverage change filter for DUP">
110 ##FILTER=<ID=COV_CHANGE_INS,Description="Coverage change filter for INS"> 111 ##FILTER=<ID=COV_CHANGE_INS,Description="Coverage change filter for INS">
111 ##FILTER=<ID=COV_CHANGE_FRAC_US,Description="Coverage fractional change filter: upstream-start"> 112 ##FILTER=<ID=COV_CHANGE_FRAC_US,Description="Coverage fractional change filter: upstream-start">
112 ##FILTER=<ID=COV_CHANGE_FRAC_SC,Description="Coverage fractional change filter: start-center"> 113 ##FILTER=<ID=COV_CHANGE_FRAC_SC,Description="Coverage fractional change filter: start-center">
113 ##FILTER=<ID=COV_CHANGE_FRAC_CE,Description="Coverage fractional change filter: center-end"> 114 ##FILTER=<ID=COV_CHANGE_FRAC_CE,Description="Coverage fractional change filter: center-end">
114 ##FILTER=<ID=COV_CHANGE_FRAC_ED,Description="Coverage fractional change filter: end-downstream"> 115 ##FILTER=<ID=COV_CHANGE_FRAC_ED,Description="Coverage fractional change filter: end-downstream">
115 ##FILTER=<ID=MOSAIC_AF,Description="Mosaic variant allele frequency filter"> 116 ##FILTER=<ID=MOSAIC_VAF,Description="Mosaic variant allele fraction filter">
116 ##FILTER=<ID=NOT_MOSAIC_AF,Description="Variant allele frequency filter for non-mosaic"> 117 ##FILTER=<ID=NOT_MOSAIC_VAF,Description="Variant allele fraction filter for non-mosaic">
117 ##FILTER=<ID=ALN_NM,Description="Length adjusted mismatch filter"> 118 ##FILTER=<ID=ALN_NM,Description="Length adjusted mismatch filter">
118 ##FILTER=<ID=STRAND_BND,Description="Strand support filter for BNDs"> 119 ##FILTER=<ID=STRAND_BND,Description="Strand support filter for BNDs">
119 ##FILTER=<ID=STRAND,Description="Strand support filter for germline SVs"> 120 ##FILTER=<ID=STRAND,Description="Strand support filter for germline SVs">
120 ##FILTER=<ID=STRAND_MOSAIC,Description="Strand support filter for mosaic SVs"> 121 ##FILTER=<ID=STRAND_MOSAIC,Description="Strand support filter for mosaic SVs">
121 ##FILTER=<ID=SVLEN_MIN,Description="SV length filter"> 122 ##FILTER=<ID=SVLEN_MIN,Description="SV length filter">
136 ##INFO=<ID=STRAND,Number=1,Type=String,Description="Strands of supporting reads for structural variant"> 137 ##INFO=<ID=STRAND,Number=1,Type=String,Description="Strands of supporting reads for structural variant">
137 ##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count, summed up over all samples"> 138 ##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count, summed up over all samples">
138 ##INFO=<ID=SUPP_VEC,Number=1,Type=String,Description="List of read support for all samples"> 139 ##INFO=<ID=SUPP_VEC,Number=1,Type=String,Description="List of read support for all samples">
139 ##INFO=<ID=CONSENSUS_SUPPORT,Number=1,Type=Integer,Description="Number of reads that support the generated insertion (INS) consensus sequence"> 140 ##INFO=<ID=CONSENSUS_SUPPORT,Number=1,Type=Integer,Description="Number of reads that support the generated insertion (INS) consensus sequence">
140 ##INFO=<ID=RNAMES,Number=.,Type=String,Description="Names of supporting reads (if enabled with --output-rnames)"> 141 ##INFO=<ID=RNAMES,Number=.,Type=String,Description="Names of supporting reads (if enabled with --output-rnames)">
141 ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> 142 ##INFO=<ID=VAF,Number=1,Type=Float,Description="Variant Allele Fraction">
142 ##INFO=<ID=NM,Number=.,Type=Float,Description="Mean number of query alignment length adjusted mismatches of supporting reads"> 143 ##INFO=<ID=NM,Number=.,Type=Float,Description="Mean number of query alignment length adjusted mismatches of supporting reads">
143 ##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"> 144 ##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">
144 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE 145 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
145 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 1/1:60:0:48 146 21 21492142 Sniffles2.DEL.0S14 N <DEL> 52 PASS PRECISE;SVTYPE=DEL;SVLEN=-506;END=21492647;SUPPORT=48;COVERAGE=46,43,43,43,48;STRAND=+-;STDEV_LEN=0.509;STDEV_POS=1.404;VAF=0.527 GT:GQ:DR:DV 0/1:60:43:48