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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
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3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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1 ##fileformat=VCFv4.2
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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2 ##source=Sniffles2_2.4
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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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"
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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4 ##fileDate="2024/09/14 14:16:58"
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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>
1
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91 ##ALT=<ID=INS,Description="Insertion">
0
93c4b04a0769 "planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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92 ##ALT=<ID=DEL,Description="Deletion">
93c4b04a0769 "planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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93 ##ALT=<ID=DUP,Description="Duplication">
93c4b04a0769 "planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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94 ##ALT=<ID=INV,Description="Inversion">
1
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95 ##ALT=<ID=BND,Description="Breakend; Translocation">
0
93c4b04a0769 "planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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96 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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97 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
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98 ##FORMAT=<ID=DR,Number=1,Type=Integer,Description="Number of reference reads">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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99 ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of variant reads">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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100 ##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phase-block, zero if none or not phased">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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101 ##FORMAT=<ID=ID,Number=1,Type=String,Description="Individual sample SV ID for multi-sample output">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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102 ##FILTER=<ID=PASS,Description="All filters passed">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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103 ##FILTER=<ID=GT,Description="Genotype filter">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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104 ##FILTER=<ID=SUPPORT_MIN,Description="Minimum read support filter">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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parents: 0
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105 ##FILTER=<ID=STDEV_POS,Description="SV Breakpoint standard deviation filter">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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106 ##FILTER=<ID=STDEV_LEN,Description="SV length standard deviation filter">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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107 ##FILTER=<ID=COV_MIN,Description="Minimum coverage filter">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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108 ##FILTER=<ID=COV_MIN_GT,Description="Minimum coverage filter (missing genotype)">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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109 ##FILTER=<ID=COV_CHANGE,Description="Coverage change filter">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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110 ##FILTER=<ID=COV_CHANGE_INS,Description="Coverage change filter for INS">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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111 ##FILTER=<ID=COV_CHANGE_FRAC_US,Description="Coverage fractional change filter: upstream-start">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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112 ##FILTER=<ID=COV_CHANGE_FRAC_SC,Description="Coverage fractional change filter: start-center">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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113 ##FILTER=<ID=COV_CHANGE_FRAC_CE,Description="Coverage fractional change filter: center-end">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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114 ##FILTER=<ID=COV_CHANGE_FRAC_ED,Description="Coverage fractional change filter: end-downstream">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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115 ##FILTER=<ID=MOSAIC_AF,Description="Mosaic variant allele frequency filter">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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116 ##FILTER=<ID=NOT_MOSAIC_AF,Description="Variant allele frequency filter for non-mosaic">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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parents: 0
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117 ##FILTER=<ID=ALN_NM,Description="Length adjusted mismatch filter">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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118 ##FILTER=<ID=STRAND_BND,Description="Strand support filter for BNDs">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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119 ##FILTER=<ID=STRAND,Description="Strand support filter for germline SVs">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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120 ##FILTER=<ID=STRAND_MOSAIC,Description="Strand support filter for mosaic SVs">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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121 ##FILTER=<ID=SVLEN_MIN,Description="SV length filter">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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diff changeset
122 ##FILTER=<ID=SVLEN_MIN_MOSAIC,Description="SV length filter for mosaic SVs">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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123 ##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Structural variation with precise breakpoints">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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124 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Structural variation with imprecise breakpoints">
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125 ##INFO=<ID=MOSAIC,Number=0,Type=Flag,Description="Structural variation classified as putative mosaic">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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126 ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of structural variation">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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127 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variation">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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128 ##INFO=<ID=CHR2,Number=1,Type=String,Description="Mate chromsome for BND SVs">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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129 ##INFO=<ID=SUPPORT,Number=1,Type=Integer,Description="Number of reads supporting the structural variation">
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130 ##INFO=<ID=SUPPORT_INLINE,Number=1,Type=Integer,Description="Number of reads supporting an INS/DEL SV (non-split events only)">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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131 ##INFO=<ID=SUPPORT_LONG,Number=1,Type=Integer,Description="Number of soft-clipped reads putatively supporting the long insertion SV">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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132 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of structural variation">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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133 ##INFO=<ID=STDEV_POS,Number=1,Type=Float,Description="Standard deviation of structural variation start position">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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134 ##INFO=<ID=STDEV_LEN,Number=1,Type=Float,Description="Standard deviation of structural variation length">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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135 ##INFO=<ID=COVERAGE,Number=.,Type=Float,Description="Coverages near upstream, start, center, end, downstream of structural variation">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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parents: 0
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136 ##INFO=<ID=STRAND,Number=1,Type=String,Description="Strands of supporting reads for structural variant">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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137 ##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count, summed up over all samples">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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138 ##INFO=<ID=SUPP_VEC,Number=1,Type=String,Description="List of read support for all samples">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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139 ##INFO=<ID=CONSENSUS_SUPPORT,Number=1,Type=Integer,Description="Number of reads that support the generated insertion (INS) consensus sequence">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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140 ##INFO=<ID=RNAMES,Number=.,Type=String,Description="Names of supporting reads (if enabled with --output-rnames)">
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141 ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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142 ##INFO=<ID=NM,Number=.,Type=Float,Description="Mean number of query alignment length adjusted mismatches of supporting reads">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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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">
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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144 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
3f6f028f418f planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
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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