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annotate test-data/expected_outcome6.vcf @ 3:09f5c6f3088a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
author iuc
date Thu, 26 Sep 2024 11:44:13 +0000
parents 93c4b04a0769
children 43fffeed243f
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09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
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1 ##fileformat=VCFv4.2
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
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2 ##source=Sniffles2_2.4
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
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3 ##command="/home/ross/miniconda3/envs/__sniffles@2.4/bin/sniffles -t 1 -i input.bam -v /tmp/tmpy46o57ly/job_working_directory/000/13/outputs/dataset_43c28376-bced-457b-9bc3-79b482047f0a.dat --allow-overwrite --reference /tmp/tmpy46o57ly/files/d/8/7/dataset_d879002d-9f55-45f7-a278-e6c9b6881fe8.dat --minsupport auto --max-splits-kb 0.1 --minsvlen 50 --mapq 20 --min-alignment-length 100 --cluster-binsize 100 --cluster-r 2.5"
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
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4 ##fileDate="2024/09/26 18:24:13"
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93c4b04a0769 "planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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88 ##contig=<ID=GL000192.1,length=547496>
93c4b04a0769 "planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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89 ##contig=<ID=NC_007605,length=171823>
93c4b04a0769 "planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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90 ##contig=<ID=hs37d5,length=35477943>
3
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
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parents: 0
diff changeset
91 ##ALT=<ID=INS,Description="Insertion">
0
93c4b04a0769 "planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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92 ##ALT=<ID=DEL,Description="Deletion">
93c4b04a0769 "planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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diff changeset
93 ##ALT=<ID=DUP,Description="Duplication">
93c4b04a0769 "planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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diff changeset
94 ##ALT=<ID=INV,Description="Inversion">
3
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
95 ##ALT=<ID=BND,Description="Breakend; Translocation">
0
93c4b04a0769 "planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
iuc
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diff changeset
96 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
3
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
97 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
98 ##FORMAT=<ID=DR,Number=1,Type=Integer,Description="Number of reference reads">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
99 ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of variant reads">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
100 ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phase-block, zero if none or not phased">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
101 ##FORMAT=<ID=ID,Number=1,Type=String,Description="Individual sample SV ID for multi-sample output">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
102 ##FILTER=<ID=PASS,Description="All filters passed">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
103 ##FILTER=<ID=GT,Description="Genotype filter">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
104 ##FILTER=<ID=SUPPORT_MIN,Description="Minimum read support filter">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
105 ##FILTER=<ID=STDEV_POS,Description="SV Breakpoint standard deviation filter">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
106 ##FILTER=<ID=STDEV_LEN,Description="SV length standard deviation filter">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
107 ##FILTER=<ID=COV_MIN,Description="Minimum coverage filter">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
108 ##FILTER=<ID=COV_MIN_GT,Description="Minimum coverage filter (missing genotype)">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
109 ##FILTER=<ID=COV_CHANGE,Description="Coverage change filter">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
110 ##FILTER=<ID=COV_CHANGE_INS,Description="Coverage change filter for INS">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
111 ##FILTER=<ID=COV_CHANGE_FRAC_US,Description="Coverage fractional change filter: upstream-start">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
112 ##FILTER=<ID=COV_CHANGE_FRAC_SC,Description="Coverage fractional change filter: start-center">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
113 ##FILTER=<ID=COV_CHANGE_FRAC_CE,Description="Coverage fractional change filter: center-end">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
114 ##FILTER=<ID=COV_CHANGE_FRAC_ED,Description="Coverage fractional change filter: end-downstream">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
115 ##FILTER=<ID=MOSAIC_AF,Description="Mosaic variant allele frequency filter">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
116 ##FILTER=<ID=NOT_MOSAIC_AF,Description="Variant allele frequency filter for non-mosaic">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
117 ##FILTER=<ID=ALN_NM,Description="Length adjusted mismatch filter">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
118 ##FILTER=<ID=STRAND_BND,Description="Strand support filter for BNDs">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
119 ##FILTER=<ID=STRAND,Description="Strand support filter for germline SVs">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
120 ##FILTER=<ID=STRAND_MOSAIC,Description="Strand support filter for mosaic SVs">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
121 ##FILTER=<ID=SVLEN_MIN,Description="SV length filter">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
122 ##FILTER=<ID=SVLEN_MIN_MOSAIC,Description="SV length filter for mosaic SVs">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
123 ##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Structural variation with precise breakpoints">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
124 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Structural variation with imprecise breakpoints">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
125 ##INFO=<ID=MOSAIC,Number=0,Type=Flag,Description="Structural variation classified as putative mosaic">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
126 ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of structural variation">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
127 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variation">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
128 ##INFO=<ID=CHR2,Number=1,Type=String,Description="Mate chromsome for BND SVs">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
129 ##INFO=<ID=SUPPORT,Number=1,Type=Integer,Description="Number of reads supporting the structural variation">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
130 ##INFO=<ID=SUPPORT_INLINE,Number=1,Type=Integer,Description="Number of reads supporting an INS/DEL SV (non-split events only)">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
131 ##INFO=<ID=SUPPORT_LONG,Number=1,Type=Integer,Description="Number of soft-clipped reads putatively supporting the long insertion SV">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
132 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of structural variation">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
133 ##INFO=<ID=STDEV_POS,Number=1,Type=Float,Description="Standard deviation of structural variation start position">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
134 ##INFO=<ID=STDEV_LEN,Number=1,Type=Float,Description="Standard deviation of structural variation length">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
135 ##INFO=<ID=COVERAGE,Number=.,Type=Float,Description="Coverages near upstream, start, center, end, downstream of structural variation">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
136 ##INFO=<ID=STRAND,Number=1,Type=String,Description="Strands of supporting reads for structural variant">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
137 ##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count, summed up over all samples">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
138 ##INFO=<ID=SUPP_VEC,Number=1,Type=String,Description="List of read support for all samples">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
139 ##INFO=<ID=CONSENSUS_SUPPORT,Number=1,Type=Integer,Description="Number of reads that support the generated insertion (INS) consensus sequence">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
140 ##INFO=<ID=RNAMES,Number=.,Type=String,Description="Names of supporting reads (if enabled with --output-rnames)">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
141 ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
142 ##INFO=<ID=NM,Number=.,Type=Float,Description="Mean number of query alignment length adjusted mismatches of supporting reads">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
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">
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
144 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
09f5c6f3088a planemo upload for repository https://github.com/galaxyproject/tools-iuc commit efa9995b93e5f32a148d9c3cf65a008543e5a6b4
iuc
parents: 0
diff changeset
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