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comparison test-data/expected_outcome4.vcf @ 1:3f6f028f418f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
author iuc
date Tue, 24 Sep 2024 19:30:03 +0000
parents 93c4b04a0769
children 09f5c6f3088a
comparison
equal deleted inserted replaced
0:93c4b04a0769 1:3f6f028f418f
1 ##fileformat=VCFv4.1 1 ##fileformat=VCFv4.2
2 ##source=Sniffles 2 ##source=Sniffles2_2.4
3 ##fileDate=20200901:51:57 AMef_minus 3 ##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpxu4n4sep/job_working_directory/000/8/outputs/dataset_b4585ddd-d52d-4087-9461-cb14a87c00d4.dat --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 5 --cluster-r 2.5 --allow-overwrite"
4 ##fileDate="2024/09/14 14:16:58"
4 ##contig=<ID=1,length=249250621> 5 ##contig=<ID=1,length=249250621>
5 ##contig=<ID=2,length=243199373> 6 ##contig=<ID=2,length=243199373>
6 ##contig=<ID=3,length=198022430> 7 ##contig=<ID=3,length=198022430>
7 ##contig=<ID=4,length=191154276> 8 ##contig=<ID=4,length=191154276>
8 ##contig=<ID=5,length=180915260> 9 ##contig=<ID=5,length=180915260>
85 ##contig=<ID=GL000194.1,length=191469> 86 ##contig=<ID=GL000194.1,length=191469>
86 ##contig=<ID=GL000225.1,length=211173> 87 ##contig=<ID=GL000225.1,length=211173>
87 ##contig=<ID=GL000192.1,length=547496> 88 ##contig=<ID=GL000192.1,length=547496>
88 ##contig=<ID=NC_007605,length=171823> 89 ##contig=<ID=NC_007605,length=171823>
89 ##contig=<ID=hs37d5,length=35477943> 90 ##contig=<ID=hs37d5,length=35477943>
91 ##ALT=<ID=INS,Description="Insertion">
90 ##ALT=<ID=DEL,Description="Deletion"> 92 ##ALT=<ID=DEL,Description="Deletion">
91 ##ALT=<ID=DUP,Description="Duplication"> 93 ##ALT=<ID=DUP,Description="Duplication">
92 ##ALT=<ID=INV,Description="Inversion"> 94 ##ALT=<ID=INV,Description="Inversion">
93 ##ALT=<ID=INVDUP,Description="InvertedDUP with unknown boundaries"> 95 ##ALT=<ID=BND,Description="Breakend; Translocation">
94 ##ALT=<ID=TRA,Description="Translocation">
95 ##ALT=<ID=INS,Description="Insertion">
96 ##FILTER=<ID=UNRESOLVED,Description="An insertion that is longer than the read and thus we cannot predict the full size.">
97 ##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for END coordinate in case of a translocation">
98 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant">
99 ##INFO=<ID=MAPQ,Number=1,Type=Integer,Description="Median mapping quality of paired-ends">
100 ##INFO=<ID=RE,Number=1,Type=Integer,Description="read support">
101 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
102 ##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variation">
103 ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of the SV">
104 ##INFO=<ID=SVMETHOD,Number=1,Type=String,Description="Type of approach used to detect SV">
105 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
106 ##INFO=<ID=SEQ,Number=1,Type=String,Description="Extracted sequence from the best representative read.">
107 ##INFO=<ID=STRANDS2,Number=4,Type=Integer,Description="alt reads first + ,alt reads first -,alt reads second + ,alt reads second -.">
108 ##INFO=<ID=REF_strand,Number=.,Type=Integer,Description="plus strand ref, minus strand ref.">
109 ##INFO=<ID=Strandbias_pval,Number=A,Type=Float,Description="P-value for fisher exact test for strand bias.">
110 ##INFO=<ID=STD_quant_start,Number=A,Type=Float,Description="STD of the start breakpoints across the reads.">
111 ##INFO=<ID=STD_quant_stop,Number=A,Type=Float,Description="STD of the stop breakpoints across the reads.">
112 ##INFO=<ID=Kurtosis_quant_start,Number=A,Type=Float,Description="Kurtosis value of the start breakpoints across the reads.">
113 ##INFO=<ID=Kurtosis_quant_stop,Number=A,Type=Float,Description="Kurtosis value of the stop breakpoints across the reads.">
114 ##INFO=<ID=SUPTYPE,Number=.,Type=String,Description="Type by which the variant is supported.(SR,AL,NR)">
115 ##INFO=<ID=STRANDS,Number=A,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">
116 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency.">
117 ##INFO=<ID=ZMW,Number=A,Type=Integer,Description="Number of ZMWs (Pacbio) supporting SV.">
118 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 96 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
119 ##FORMAT=<ID=DR,Number=1,Type=Integer,Description="# high-quality reference reads"> 97 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
120 ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality variant reads"> 98 ##FORMAT=<ID=DR,Number=1,Type=Integer,Description="Number of reference reads">
121 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT input.bam 99 ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of variant reads">
122 21 21492143 0 AAAATATGTTTTAAATTGTTGATGATTTCAAATATTACAGGAATAGAAACTTTAACTTAACACAGAATGATTATCTGGCTTCCTTCTGTAAAATATCTTAAAGGTTAATGTGGATTTGAATTGCACAACATTCCAAATGCTTCTCCCCCTTTAAAAAGAATAGTCTTATCTTTTAAAAAGAATACTCATATCTTTTATTTTTCTTATGCAAGAGCAAAAATAAGGAAAAAATATATTATTCAGGAGAATCATGGCAACAATTTAAGGAAGACAAAACCAGTCTTTAGCAACCAGTATACATATATATCATCTTTTTTTCTGCTTTAGGGTAGGTTGCTTCTATCACCAACCTGTTCCAAATCCTCCTCTTACATGCACCATTAAAACATACTCTTTCAAAAACGAGGTGATAAAATCACAAATATCAATCTATCGTTCAGAAGAAGGTACCTTTATTTTACCTTAAAGGAATTTGATATATAATGGAGAAAAGAAAATTACTTTCT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=21;END=21492649;STD_quant_start=0.000000;STD_quant_stop=0.000000;Kurtosis_quant_start=0.572582;Kurtosis_quant_stop=1.417662;SVTYPE=DEL;SUPTYPE=AL,SR;SVLEN=-506;STRANDS=+-;STRANDS2=22,26,22,26;RE=48;REF_strand=19,24;Strandbias_pval=1;AF=0.527473 GT:DR:DV 0/1:43:48 100 ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phase-block, zero if none or not phased">
101 ##FORMAT=<ID=ID,Number=1,Type=String,Description="Individual sample SV ID for multi-sample output">
102 ##FILTER=<ID=PASS,Description="All filters passed">
103 ##FILTER=<ID=GT,Description="Genotype filter">
104 ##FILTER=<ID=SUPPORT_MIN,Description="Minimum read support filter">
105 ##FILTER=<ID=STDEV_POS,Description="SV Breakpoint standard deviation filter">
106 ##FILTER=<ID=STDEV_LEN,Description="SV length standard deviation filter">
107 ##FILTER=<ID=COV_MIN,Description="Minimum coverage filter">
108 ##FILTER=<ID=COV_MIN_GT,Description="Minimum coverage filter (missing genotype)">
109 ##FILTER=<ID=COV_CHANGE,Description="Coverage change filter">
110 ##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_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_ED,Description="Coverage fractional change filter: end-downstream">
115 ##FILTER=<ID=MOSAIC_AF,Description="Mosaic variant allele frequency filter">
116 ##FILTER=<ID=NOT_MOSAIC_AF,Description="Variant allele frequency filter for non-mosaic">
117 ##FILTER=<ID=ALN_NM,Description="Length adjusted mismatch filter">
118 ##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_MOSAIC,Description="Strand support filter for mosaic SVs">
121 ##FILTER=<ID=SVLEN_MIN,Description="SV length filter">
122 ##FILTER=<ID=SVLEN_MIN_MOSAIC,Description="SV length filter for mosaic SVs">
123 ##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Structural variation with precise breakpoints">
124 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Structural variation with imprecise breakpoints">
125 ##INFO=<ID=MOSAIC,Number=0,Type=Flag,Description="Structural variation classified as putative mosaic">
126 ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of structural variation">
127 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variation">
128 ##INFO=<ID=CHR2,Number=1,Type=String,Description="Mate chromsome for BND SVs">
129 ##INFO=<ID=SUPPORT,Number=1,Type=Integer,Description="Number of reads supporting the structural variation">
130 ##INFO=<ID=SUPPORT_INLINE,Number=1,Type=Integer,Description="Number of reads supporting an INS/DEL SV (non-split events only)">
131 ##INFO=<ID=SUPPORT_LONG,Number=1,Type=Integer,Description="Number of soft-clipped reads putatively supporting the long insertion SV">
132 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of structural variation">
133 ##INFO=<ID=STDEV_POS,Number=1,Type=Float,Description="Standard deviation of structural variation start position">
134 ##INFO=<ID=STDEV_LEN,Number=1,Type=Float,Description="Standard deviation of structural variation length">
135 ##INFO=<ID=COVERAGE,Number=.,Type=Float,Description="Coverages near upstream, start, center, end, downstream of structural variation">
136 ##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=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=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=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 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
145 21 21492142 Sniffles2.DEL.1S14 N <DEL> 52 PASS PRECISE;SVTYPE=DEL;SVLEN=-506;END=21492648;SUPPORT=47;COVERAGE=48,43,43,43,51;STRAND=+-;AF=1.000;STDEV_LEN=0.500;STDEV_POS=1.384 GT:GQ:DR:DV 1/1:60:0:47