Mercurial > repos > iuc > sniffles
comparison test-data/expected_outcome4.vcf @ 0:93c4b04a0769 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc commit f5977355970ef4994957147d2d8a96fe6605e2b4"
author | iuc |
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date | Mon, 14 Sep 2020 07:39:07 +0000 |
parents | |
children | 3f6f028f418f |
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-1:000000000000 | 0:93c4b04a0769 |
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1 ##fileformat=VCFv4.1 | |
2 ##source=Sniffles | |
3 ##fileDate=20200901:51:57 AMef_minus | |
4 ##contig=<ID=1,length=249250621> | |
5 ##contig=<ID=2,length=243199373> | |
6 ##contig=<ID=3,length=198022430> | |
7 ##contig=<ID=4,length=191154276> | |
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71 ##contig=<ID=GL000211.1,length=166566> | |
72 ##contig=<ID=GL000199.1,length=169874> | |
73 ##contig=<ID=GL000217.1,length=172149> | |
74 ##contig=<ID=GL000216.1,length=172294> | |
75 ##contig=<ID=GL000215.1,length=172545> | |
76 ##contig=<ID=GL000205.1,length=174588> | |
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78 ##contig=<ID=GL000224.1,length=179693> | |
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80 ##contig=<ID=GL000195.1,length=182896> | |
81 ##contig=<ID=GL000212.1,length=186858> | |
82 ##contig=<ID=GL000222.1,length=186861> | |
83 ##contig=<ID=GL000200.1,length=187035> | |
84 ##contig=<ID=GL000193.1,length=189789> | |
85 ##contig=<ID=GL000194.1,length=191469> | |
86 ##contig=<ID=GL000225.1,length=211173> | |
87 ##contig=<ID=GL000192.1,length=547496> | |
88 ##contig=<ID=NC_007605,length=171823> | |
89 ##contig=<ID=hs37d5,length=35477943> | |
90 ##ALT=<ID=DEL,Description="Deletion"> | |
91 ##ALT=<ID=DUP,Description="Duplication"> | |
92 ##ALT=<ID=INV,Description="Inversion"> | |
93 ##ALT=<ID=INVDUP,Description="InvertedDUP with unknown boundaries"> | |
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"> | |
119 ##FORMAT=<ID=DR,Number=1,Type=Integer,Description="# high-quality reference reads"> | |
120 ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality variant reads"> | |
121 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT input.bam | |
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 |