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"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
author iuc
date Mon, 14 Sep 2020 07:39:07 +0000
parents
children 3f6f028f418f
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93c4b04a0769 "planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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93c4b04a0769 "planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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93c4b04a0769 "planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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90 ##ALT=<ID=DEL,Description="Deletion">
93c4b04a0769 "planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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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">
93c4b04a0769 "planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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96 ##FILTER=<ID=UNRESOLVED,Description="An insertion that is longer than the read and thus we cannot predict the full size.">
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97 ##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for END coordinate in case of a translocation">
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98 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant">
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99 ##INFO=<ID=MAPQ,Number=1,Type=Integer,Description="Median mapping quality of paired-ends">
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100 ##INFO=<ID=RE,Number=1,Type=Integer,Description="read support">
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101 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
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102 ##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variation">
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103 ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of the SV">
93c4b04a0769 "planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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104 ##INFO=<ID=SVMETHOD,Number=1,Type=String,Description="Type of approach used to detect SV">
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105 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
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106 ##INFO=<ID=SEQ,Number=1,Type=String,Description="Extracted sequence from the best representative read.">
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107 ##INFO=<ID=STRANDS2,Number=4,Type=Integer,Description="alt reads first + ,alt reads first -,alt reads second + ,alt reads second -.">
93c4b04a0769 "planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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108 ##INFO=<ID=REF_strand,Number=.,Type=Integer,Description="plus strand ref, minus strand ref.">
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109 ##INFO=<ID=Strandbias_pval,Number=A,Type=Float,Description="P-value for fisher exact test for strand bias.">
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110 ##INFO=<ID=STD_quant_start,Number=A,Type=Float,Description="STD of the start breakpoints across the reads.">
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111 ##INFO=<ID=STD_quant_stop,Number=A,Type=Float,Description="STD of the stop breakpoints across the reads.">
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112 ##INFO=<ID=Kurtosis_quant_start,Number=A,Type=Float,Description="Kurtosis value of the start breakpoints across the reads.">
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113 ##INFO=<ID=Kurtosis_quant_stop,Number=A,Type=Float,Description="Kurtosis value of the stop breakpoints across the reads.">
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114 ##INFO=<ID=SUPTYPE,Number=.,Type=String,Description="Type by which the variant is supported.(SR,AL,NR)">
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115 ##INFO=<ID=STRANDS,Number=A,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">
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116 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency.">
93c4b04a0769 "planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
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117 ##INFO=<ID=ZMW,Number=A,Type=Integer,Description="Number of ZMWs (Pacbio) supporting SV.">
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118 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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119 ##FORMAT=<ID=DR,Number=1,Type=Integer,Description="# high-quality reference reads">
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120 ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality variant reads">
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121 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT input.bam
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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