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comparison test-data/expected_output2.vcf @ 0:93c4b04a0769 draft

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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
comparison
equal deleted inserted replaced
-1:000000000000 0:93c4b04a0769
1 ##fileformat=VCFv4.1
2 ##source=Sniffles
3 ##fileDate=20200901:51:36 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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11 ##contig=<ID=8,length=146364022>
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25 ##contig=<ID=22,length=51304566>
26 ##contig=<ID=X,length=155270560>
27 ##contig=<ID=Y,length=59373566>
28 ##contig=<ID=MT,length=16569>
29 ##contig=<ID=GL000207.1,length=4262>
30 ##contig=<ID=GL000226.1,length=15008>
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56 ##contig=<ID=GL000230.1,length=43691>
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60 ##contig=<ID=GL000198.1,length=90085>
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62 ##contig=<ID=GL000191.1,length=106433>
63 ##contig=<ID=GL000227.1,length=128374>
64 ##contig=<ID=GL000228.1,length=129120>
65 ##contig=<ID=GL000214.1,length=137718>
66 ##contig=<ID=GL000221.1,length=155397>
67 ##contig=<ID=GL000209.1,length=159169>
68 ##contig=<ID=GL000218.1,length=161147>
69 ##contig=<ID=GL000220.1,length=161802>
70 ##contig=<ID=GL000213.1,length=164239>
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>
77 ##contig=<ID=GL000219.1,length=179198>
78 ##contig=<ID=GL000224.1,length=179693>
79 ##contig=<ID=GL000223.1,length=180455>
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=RNAMES,Number=.,Type=String,Description="Names of reads supporting SVs (comma separated)">
107 ##INFO=<ID=SEQ,Number=1,Type=String,Description="Extracted sequence from the best representative read.">
108 ##INFO=<ID=STRANDS2,Number=4,Type=Integer,Description="alt reads first + ,alt reads first -,alt reads second + ,alt reads second -.">
109 ##INFO=<ID=REF_strand,Number=.,Type=Integer,Description="plus strand ref, minus strand ref.">
110 ##INFO=<ID=Strandbias_pval,Number=A,Type=Float,Description="P-value for fisher exact test for strand bias.">
111 ##INFO=<ID=STD_quant_start,Number=A,Type=Float,Description="STD of the start breakpoints across the reads.">
112 ##INFO=<ID=STD_quant_stop,Number=A,Type=Float,Description="STD of the stop breakpoints across the reads.">
113 ##INFO=<ID=Kurtosis_quant_start,Number=A,Type=Float,Description="Kurtosis value of the start breakpoints across the reads.">
114 ##INFO=<ID=Kurtosis_quant_stop,Number=A,Type=Float,Description="Kurtosis value of the stop breakpoints across the reads.">
115 ##INFO=<ID=SUPTYPE,Number=.,Type=String,Description="Type by which the variant is supported.(SR,AL,NR)">
116 ##INFO=<ID=STRANDS,Number=A,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">
117 ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency.">
118 ##INFO=<ID=ZMW,Number=A,Type=Integer,Description="Number of ZMWs (Pacbio) supporting SV.">
119 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
120 ##FORMAT=<ID=DR,Number=1,Type=Integer,Description="# high-quality reference reads">
121 ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality variant reads">
122 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT input.bam
123 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;RNAMES=21_21470395_-,21_21478921_-,21_21480008_-,21_21480363_-,21_21481423_-,21_21481887_+,21_21482167_+,21_21482571_-,21_21483235_+,21_21484045_+,21_21484064_-,21_21484222_+,21_21484629_-,21_21485143_+,21_21485316_+,21_21486018_+,21_21486410_+,21_21486549_+,21_21486783_-,21_21487049_+,21_21487332_-,21_21487543_-,21_21487743_+,21_21487803_-,21_21487987_-,21_21488230_-,21_21488258_-,21_21488405_+,21_21488511_-,21_21488850_-,21_21489305_+,21_21489335_-,21_21489385_-,21_21489559_-,21_21489628_+,21_21490045_+,21_21490154_+,21_21490154_-,21_21490705_+,21_21491059_-,21_21491140_-,21_21491170_+,21_21491195_-,21_21491512_-,21_21491645_-,21_21491660_+,21_21491808_+,21_21491999_+;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