Mercurial > repos > iuc > delly_lr

comparison test-data/call_1.vcf.gz @ 0:629a0066003d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
author iuc
date Mon, 28 Sep 2020 07:45:41 +0000
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-1:000000000000 0:629a0066003d
1 ##fileformat=VCFv4.2
2 ##FILTER=<ID=PASS,Description="All filters passed">
3 ##fileDate=20200728
4 ##ALT=<ID=DEL,Description="Deletion">
5 ##ALT=<ID=DUP,Description="Duplication">
6 ##ALT=<ID=INV,Description="Inversion">
7 ##ALT=<ID=BND,Description="Translocation">
8 ##ALT=<ID=INS,Description="Insertion">
9 ##FILTER=<ID=LowQual,Description="Poor quality and insufficient number of PEs and SRs.">
10 ##INFO=<ID=CIEND,Number=2,Type=Integer,Description="PE confidence interval around END">
11 ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="PE confidence interval around POS">
12 ##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for POS2 coordinate in case of an inter-chromosomal translocation">
13 ##INFO=<ID=POS2,Number=1,Type=Integer,Description="Genomic position for CHR2 in case of an inter-chromosomal translocation">
14 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant">
15 ##INFO=<ID=PE,Number=1,Type=Integer,Description="Paired-end support of the structural variant">
16 ##INFO=<ID=MAPQ,Number=1,Type=Integer,Description="Median mapping quality of paired-ends">
17 ##INFO=<ID=SRMAPQ,Number=1,Type=Integer,Description="Median mapping quality of split-reads">
18 ##INFO=<ID=SR,Number=1,Type=Integer,Description="Split-read support">
19 ##INFO=<ID=SRQ,Number=1,Type=Float,Description="Split-read consensus alignment quality">
20 ##INFO=<ID=CONSENSUS,Number=1,Type=String,Description="Split-read consensus sequence">
21 ##INFO=<ID=CE,Number=1,Type=Float,Description="Consensus sequence entropy">
22 ##INFO=<ID=CT,Number=1,Type=String,Description="Paired-end signature induced connection type">
23 ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Insertion length for SVTYPE=INS.">
24 ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
25 ##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variation">
26 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
27 ##INFO=<ID=SVMETHOD,Number=1,Type=String,Description="Type of approach used to detect SV">
28 ##INFO=<ID=INSLEN,Number=1,Type=Integer,Description="Predicted length of the insertion">
29 ##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Predicted microhomology length using a max. edit distance of 2">
30 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
31 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Log10-scaled genotype likelihoods for RR,RA,AA genotypes">
32 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
33 ##FORMAT=<ID=FT,Number=1,Type=String,Description="Per-sample genotype filter">
34 ##FORMAT=<ID=RC,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the SV">
35 ##FORMAT=<ID=RCL,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the left control region">
36 ##FORMAT=<ID=RCR,Number=1,Type=Integer,Description="Raw high-quality read counts or base counts for the right control region">
37 ##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Read-depth based copy-number estimate for autosomal sites">
38 ##FORMAT=<ID=DR,Number=1,Type=Integer,Description="# high-quality reference pairs">
39 ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality variant pairs">
40 ##FORMAT=<ID=RR,Number=1,Type=Integer,Description="# high-quality reference junction reads">
41 ##FORMAT=<ID=RV,Number=1,Type=Integer,Description="# high-quality variant junction reads">
42 ##reference=../data/v1/genome.fasta
43 ##contig=<ID=chr10,length=135534747>
44 ##contig=<ID=chr11,length=135006516>
45 ##contig=<ID=chr11_gl000202_random,length=40103>
46 ##contig=<ID=chr12,length=133851895>
47 ##contig=<ID=chr13,length=115169878>
48 ##contig=<ID=chr14,length=107349540>
49 ##contig=<ID=chr15,length=102531392>
50 ##contig=<ID=chr16,length=90354753>
51 ##contig=<ID=chr17_ctg5_hap1,length=1680828>
52 ##contig=<ID=chr17,length=81195210>
53 ##contig=<ID=chr17_gl000203_random,length=37498>
54 ##contig=<ID=chr17_gl000204_random,length=81310>
55 ##contig=<ID=chr17_gl000205_random,length=174588>
56 ##contig=<ID=chr17_gl000206_random,length=41001>
57 ##contig=<ID=chr18,length=78077248>
58 ##contig=<ID=chr18_gl000207_random,length=4262>
59 ##contig=<ID=chr19,length=59128983>
60 ##contig=<ID=chr19_gl000208_random,length=92689>
61 ##contig=<ID=chr19_gl000209_random,length=159169>
62 ##contig=<ID=chr1,length=249250621>
63 ##contig=<ID=chr1_gl000191_random,length=106433>
64 ##contig=<ID=chr1_gl000192_random,length=547496>
65 ##contig=<ID=chr20,length=63025520>
66 ##contig=<ID=chr21,length=48129895>
67 ##contig=<ID=chr21_gl000210_random,length=27682>
68 ##contig=<ID=chr22,length=51304566>
69 ##contig=<ID=chr2,length=243199373>
70 ##contig=<ID=chr3,length=198022430>
71 ##contig=<ID=chr4_ctg9_hap1,length=590426>
72 ##contig=<ID=chr4,length=191154276>
73 ##contig=<ID=chr4_gl000193_random,length=189789>
74 ##contig=<ID=chr4_gl000194_random,length=191469>
75 ##contig=<ID=chr5,length=180915260>
76 ##contig=<ID=chr6_apd_hap1,length=4622290>
77 ##contig=<ID=chr6_cox_hap2,length=4795371>
78 ##contig=<ID=chr6_dbb_hap3,length=4610396>
79 ##contig=<ID=chr6,length=171115067>
80 ##contig=<ID=chr6_mann_hap4,length=4683263>
81 ##contig=<ID=chr6_mcf_hap5,length=4833398>
82 ##contig=<ID=chr6_qbl_hap6,length=4611984>
83 ##contig=<ID=chr6_ssto_hap7,length=4928567>
84 ##contig=<ID=chr7,length=159138663>
85 ##contig=<ID=chr7_gl000195_random,length=182896>
86 ##contig=<ID=chr8,length=146364022>
87 ##contig=<ID=chr8_gl000196_random,length=38914>
88 ##contig=<ID=chr8_gl000197_random,length=37175>
89 ##contig=<ID=chr9,length=141213431>
90 ##contig=<ID=chr9_gl000198_random,length=90085>
91 ##contig=<ID=chr9_gl000199_random,length=169874>
92 ##contig=<ID=chr9_gl000200_random,length=187035>
93 ##contig=<ID=chr9_gl000201_random,length=36148>
94 ##contig=<ID=chrM,length=16571>
95 ##contig=<ID=chrUn_gl000211,length=166566>
96 ##contig=<ID=chrUn_gl000212,length=186858>
97 ##contig=<ID=chrUn_gl000213,length=164239>
98 ##contig=<ID=chrUn_gl000214,length=137718>
99 ##contig=<ID=chrUn_gl000215,length=172545>
100 ##contig=<ID=chrUn_gl000216,length=172294>
101 ##contig=<ID=chrUn_gl000217,length=172149>
102 ##contig=<ID=chrUn_gl000218,length=161147>
103 ##contig=<ID=chrUn_gl000219,length=179198>
104 ##contig=<ID=chrUn_gl000220,length=161802>
105 ##contig=<ID=chrUn_gl000221,length=155397>
106 ##contig=<ID=chrUn_gl000222,length=186861>
107 ##contig=<ID=chrUn_gl000223,length=180455>
108 ##contig=<ID=chrUn_gl000224,length=179693>
109 ##contig=<ID=chrUn_gl000225,length=211173>
110 ##contig=<ID=chrUn_gl000226,length=15008>
111 ##contig=<ID=chrUn_gl000227,length=128374>
112 ##contig=<ID=chrUn_gl000228,length=129120>
113 ##contig=<ID=chrUn_gl000229,length=19913>
114 ##contig=<ID=chrUn_gl000230,length=43691>
115 ##contig=<ID=chrUn_gl000231,length=27386>
116 ##contig=<ID=chrUn_gl000232,length=40652>
117 ##contig=<ID=chrUn_gl000233,length=45941>
118 ##contig=<ID=chrUn_gl000234,length=40531>
119 ##contig=<ID=chrUn_gl000235,length=34474>
120 ##contig=<ID=chrUn_gl000236,length=41934>
121 ##contig=<ID=chrUn_gl000237,length=45867>
122 ##contig=<ID=chrUn_gl000238,length=39939>
123 ##contig=<ID=chrUn_gl000239,length=33824>
124 ##contig=<ID=chrUn_gl000240,length=41933>
125 ##contig=<ID=chrUn_gl000241,length=42152>
126 ##contig=<ID=chrUn_gl000242,length=43523>
127 ##contig=<ID=chrUn_gl000243,length=43341>
128 ##contig=<ID=chrUn_gl000244,length=39929>
129 ##contig=<ID=chrUn_gl000245,length=36651>
130 ##contig=<ID=chrUn_gl000246,length=38154>
131 ##contig=<ID=chrUn_gl000247,length=36422>
132 ##contig=<ID=chrUn_gl000248,length=39786>
133 ##contig=<ID=chrUn_gl000249,length=38502>
134 ##contig=<ID=chrX,length=155270560>
135 ##contig=<ID=chrY,length=59373566>
136 ##bcftools_viewVersion=1.10.2+htslib-1.10.2
137 ##bcftools_viewCommand=view -Ov call_1.bcf.gz; Date=Sun Sep 27 02:27:42 2020
138 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
139 chr12 132969151 DEL00000000 G <DEL> 107 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=132969179;PE=0;MAPQ=0;CT=3to5;CIPOS=-20,20;CIEND=-20,20;SRMAPQ=41;INSLEN=0;HOMLEN=19;SR=3;SRQ=1;CONSENSUS=CCCCACTCTCCCCCCGGACCCTCCGGCCACCCTGCTCTCCCCCGGGACCCTCCGACCACGTTGCTCTTCCCAGGGTTCTGGCAC;CE=1.70498 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 1/1:-10.3982,-0.901271,0:10:LowQual:28:44:28:2:0:0:0:3 0/1:-11.9941,0,-5.30498:53:PASS:92:160:127:1:0:0:2:4
140 chr17 40726730 DEL00000001 C <DEL> 133 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=40726765;PE=0;MAPQ=0;CT=3to5;CIPOS=-7,7;CIEND=-7,7;SRMAPQ=50;INSLEN=0;HOMLEN=9;SR=3;SRQ=1;CONSENSUS=CTCTCTCCCTCCTTCCTTCCTTCCTTTTTCCTCCCTCCCTCCCTCTTTCTCCCTCCCTTCCCTCTTTTCCTCTCTTTCTTTCTCTGT;CE=1.07866 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 1/1:-7.79989,-0.601951,0:7:LowQual:31:1:20:0:0:0:0:2 1/1:-6.29935,-0.601408,0:7:LowQual:66:5:34:0:0:0:0:2
141 chr17 74283142 DEL00000002 C <DEL> 145 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=74283171;PE=0;MAPQ=0;CT=3to5;CIPOS=-18,18;CIEND=-18,18;SRMAPQ=50;INSLEN=0;HOMLEN=18;SR=3;SRQ=1;CONSENSUS=CCCACCCCCTGCCCACACACCACATAACACACACACACACACACGATGGGAGGGACCTAGTTTTTGATGAGAGGTGGGAGGGCAGGGCCAAGCCAG;CE=1.91042 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 1/1:-6.99973,-0.601785,0:7:LowQual:28:89:217:1:0:0:0:2 1/1:-13.3977,-1.20187,0:12:LowQual:28:10:70:0:0:0:0:4
142 chr17 79612049 DEL00000003 A <DEL> 840 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=79612086;PE=0;MAPQ=0;CT=3to5;CIPOS=-5,5;CIEND=-5,5;SRMAPQ=50;INSLEN=0;HOMLEN=8;SR=17;SRQ=1;CONSENSUS=TTCCTCTTCCCTCTGCAGGAAACTGCAGGCCAGAAGCCCCTCTCTGTGCACAGGGAGGACCAGGCGGAGGCCTGGGGCTGCAGCTGCTGTCCCCCGGAGACCAAGCAC;CE=1.9233 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 0/1:-34.0593,0,-106.559:10000:PASS:844:1944:1927:1:0:0:30:12 0/1:-235.677,0,-181.078:10000:PASS:1973:3537:4588:1:0:0:54:68
143 chr5 13830007 DEL00000004 T <DEL> 135 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=13830038;PE=0;MAPQ=0;CT=3to5;CIPOS=-6,6;CIEND=-6,6;SRMAPQ=45;INSLEN=0;HOMLEN=5;SR=3;SRQ=0.987179;CONSENSUS=CTATTCATATGATCTTTGCTTAACACCAAAAGGTTTTCCATTCAAGAAAACAGATGACATATGACCAGGGAGATGCAT;CE=1.93383 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 0/1:-14.6949,0,-2.59501:26:PASS:67:26:69:0:0:0:1:4 0/1:-3.39797,0,-3.49798:31:PASS:30:37:47:1:0:0:1:1
144 chr5 74363006 DEL00000005 C <DEL> 350 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=74363047;PE=0;MAPQ=0;CT=3to5;CIPOS=-4,4;CIEND=-4,4;SRMAPQ=50;INSLEN=0;HOMLEN=5;SR=7;SRQ=1;CONSENSUS=AAAGTGGTTTCTTGAGACAAAATCTACTCCTGGTGTGGTGATGTGAACACTTAGATGATAAAGCAGCAGCAGGGTGTAAGAGGATTGACTCCGATTTTCAA;CE=1.95354 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 0/1:-11.1851,0,-39.1848:112:PASS:382:637:460:2:0:0:11:4 0/1:-12.7889,0,-25.2888:128:PASS:279:415:490:1:0:0:7:4
145 chr5 75911568 DEL00000006 T <DEL> 745 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=75911598;PE=0;MAPQ=0;CT=3to5;CIPOS=-2,2;CIEND=-2,2;SRMAPQ=50;INSLEN=0;HOMLEN=1;SR=15;SRQ=1;CONSENSUS=TGTCTAATCACTAATGTCTTCCTTCCTGTCTAATCACTGAGTTAAGGGAAAAATAGTCATTTACTAATTCCATTTCCCCATTAAAAGCTATGTCTAAGAAAAAAAATAGTGGAGGCATTATTTAAAAC;CE=1.88992 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV 0/1:-61.5633,0,-65.3615:10000:PASS:779:810:615:1:0:0:20:18 0/1:-39.5838,0,-14.884:149:PASS:357:220:320:1:0:0:5:11
146 chr5 79865393 DEL00000007 G <DEL> 150 PASS PRECISE;SVTYPE=DEL;SVMETHOD=EMBL.DELLYv0.8.3;END=79865420;PE=0;MAPQ=0;CT=3to5;CIPOS=-29,29;CIEND=-29,29;SRMAPQ=50;INSLEN=0;HOMLEN=31;SR=3;SRQ=1;CONSENSUS=CTCCTGCTGCCCAGCTGCCGAGGCACCTGCGGAGACGCGCCCAAGTCAGCCCCTCCGACCCGCGCGCTCTTGCGGCCCAGCGCGCGCCGCT;CE=1.74972 GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV ./.:0,0,0:0:LowQual:12:0:0:0:0:0:0:0 0/1:-13.9933,0,-8.89295:89:PASS:117:172:133:1:0:0:3:4