Mercurial > repos > youyuh48 > sniffles

annotate test-data/expected_output.vcf @ 1:ba3aaae7a229 draft default tip

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planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/sniffles
author youyuh48
date Fri, 06 Sep 2019 02:15:16 -0400
parents ee65e517769d
children
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ee65e517769d planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/sniffles
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90 ##ALT=<ID=DEL,Description="Deletion">
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91 ##ALT=<ID=DUP,Description="Duplication">
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92 ##ALT=<ID=INV,Description="Inversion">
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93 ##ALT=<ID=INVDUP,Description="InvertedDUP with unknown boundaries">
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94 ##ALT=<ID=TRA,Description="Translocation">
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95 ##ALT=<ID=INS,Description="Insertion">
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96 ##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for END coordinate in case of a translocation">
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97 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant">
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98 ##INFO=<ID=MAPQ,Number=1,Type=Integer,Description="Median mapping quality of paired-ends">
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99 ##INFO=<ID=RE,Number=1,Type=Integer,Description="read support">
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100 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
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101 ##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variation">
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102 ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of the SV">
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103 ##INFO=<ID=SVMETHOD,Number=1,Type=String,Description="Type of approach used to detect SV">
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104 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
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105 ##INFO=<ID=STD_quant_start,Number=A,Type=Integer,Description="STD of the start breakpoints across the reads.">
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106 ##INFO=<ID=STD_quant_stop,Number=A,Type=Integer,Description="STD of the stop breakpoints across the reads.">
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107 ##INFO=<ID=Kurtosis_quant_start,Number=A,Type=Integer,Description="Kurtosis value of the start breakpoints accross the reads.">
ee65e517769d planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/sniffles
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108 ##INFO=<ID=Kurtosis_quant_stop,Number=A,Type=Integer,Description="Kurtosis value of the stop breakpoints accross the reads.">
ee65e517769d planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/sniffles
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109 ##INFO=<ID=SUPTYPE,Number=1,Type=String,Description="Type by which the variant is supported.(SR,ALN)">
ee65e517769d planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/sniffles
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110 ##INFO=<ID=SUPTYPE,Number=1,Type=String,Description="Type by which the variant is supported.(SR,ALN)">
ee65e517769d planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/sniffles
youyuh48
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111 ##INFO=<ID=STRANDS,Number=A,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">
ee65e517769d planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/sniffles
youyuh48
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112 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency.">
ee65e517769d planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/sniffles
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113 ##INFO=<ID=ZMW,Number=A,Type=Integer,Description="Number of ZMWs (Pacbio) supporting SV.">
ee65e517769d planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/sniffles
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114 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
ee65e517769d planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/sniffles
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115 ##FORMAT=<ID=DR,Number=1,Type=Integer,Description="# high-quality reference reads">
ee65e517769d planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/sniffles
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116 ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality variant reads">
ee65e517769d planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/sniffles
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117 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT reads_region.bam
ee65e517769d planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/sniffles
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118 21 21492142 0 N <DEL> . PASS PRECISE;SVMETHOD=Snifflesv1.0.8;CHR2=21;END=21492648;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=+-;RE=48 GT:DR:DV ./.:.:48