1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
|
##fileformat=VCFv4.1
##fileDate=20200518
##source=GenerateSVCandidates UNKNOWN
##reference=file:///home/dong.rn/home/Papenfuss_lab/projects/StructuralVariantAnnotation/GRIPper/hg19.1-M.fa
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
##contig=<ID=4,length=191154276>
##contig=<ID=5,length=180915260>
##contig=<ID=6,length=171115067>
##contig=<ID=7,length=159138663>
##contig=<ID=8,length=146364022>
##contig=<ID=9,length=141213431>
##contig=<ID=10,length=135534747>
##contig=<ID=11,length=135006516>
##contig=<ID=12,length=133851895>
##contig=<ID=13,length=115169878>
##contig=<ID=14,length=107349540>
##contig=<ID=15,length=102531392>
##contig=<ID=16,length=90354753>
##contig=<ID=17,length=81195210>
##contig=<ID=18,length=78077248>
##contig=<ID=19,length=59128983>
##contig=<ID=20,length=63025520>
##contig=<ID=21,length=48129895>
##contig=<ID=22,length=51304566>
##contig=<ID=X,length=155270560>
##contig=<ID=Y,length=59373566>
##contig=<ID=MT,length=16569>
##contig=<ID=hs37d5,length=35477943>
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END">
##INFO=<ID=CIGAR,Number=A,Type=String,Description="CIGAR alignment for each alternate indel allele">
##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakend">
##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical homology at event breakpoints">
##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical homology at event breakpoints">
##INFO=<ID=SVINSLEN,Number=.,Type=Integer,Description="Length of insertion">
##INFO=<ID=SVINSSEQ,Number=.,Type=String,Description="Sequence of insertion">
##INFO=<ID=LEFT_SVINSSEQ,Number=.,Type=String,Description="Known left side of insertion for an insertion of unknown length">
##INFO=<ID=RIGHT_SVINSSEQ,Number=.,Type=String,Description="Known right side of insertion for an insertion of unknown length">
##INFO=<ID=BND_DEPTH,Number=1,Type=Integer,Description="Read depth at local translocation breakend">
##INFO=<ID=MATE_BND_DEPTH,Number=1,Type=Integer,Description="Read depth at remote translocation mate breakend">
##INFO=<ID=JUNCTION_QUAL,Number=1,Type=Integer,Description="If the SV junction is part of an EVENT (ie. a multi-adjacency variant), this field provides the QUAL value for the adjacency in question only">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=FT,Number=1,Type=String,Description="Sample filter, 'PASS' indicates that all filters have passed for this sample">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=PR,Number=.,Type=Integer,Description="Spanning paired-read support for the ref and alt alleles in the order listed">
##FORMAT=<ID=SR,Number=.,Type=Integer,Description="Split reads for the ref and alt alleles in the order listed, for reads where P(allele|read)>0.999">
##FILTER=<ID=Ploidy,Description="For DEL & DUP variants, the genotypes of overlapping variants (with similar size) are inconsistent with diploid expectation">
##FILTER=<ID=MaxDepth,Description="Depth is greater than 3x the median chromosome depth near one or both variant breakends">
##FILTER=<ID=MaxMQ0Frac,Description="For a small variant (<1000 bases), the fraction of reads in all samples with MAPQ0 around either breakend exceeds 0.4">
##FILTER=<ID=NoPairSupport,Description="For variants significantly larger than the paired read fragment size, no paired reads support the alternate allele in any sample.">
##FILTER=<ID=MinQUAL,Description="QUAL score is less than 20">
##FILTER=<ID=SampleFT,Description="No sample passes all the sample-level filters (at the field FORMAT/FT)">
##FILTER=<ID=MinGQ,Description="GQ score is less than 15 (filter applied at sample level)">
##FILTER=<ID=HomRef,Description="homozygous reference call (filter applied at sample level)">
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=INS,Description="Insertion">
##ALT=<ID=DUP:TANDEM,Description="Tandem Duplication">
#CHROM POS ID REF ALT QUAL FILTER INFO
MT 16093 gridss39o T ]11:49883572]T 1829.48 . AS=2;ASQ=201.12915;ASRP=10;ASSR=9;CIGAR=1X239M;CQ=627.96;EVENT=gridss39;MATEID=gridss39h;RAS=1;RASQ=225.70378;REF=7;REFPAIR=2;RP=5;RPQ=86.13501;RSR=1;RSRQ=29.4252;SR=3;SRQ=85.568954;SVTYPE=BND
11 49883572 gridss39h A A[MT:16093[ 1829.48 . AS=1;ASQ=225.70378;ASRP=10;ASSR=9;BQ=24.57;BSC=1;BSCQ=24.574617;CIGAR=194M1X;CQ=627.96;EVENT=gridss39;MATEID=gridss39o;RAS=2;RASQ=201.12915;REF=9;REFPAIR=6;RP=5;RPQ=86.13501;RSR=3;RSRQ=85.568954;SR=1;SRQ=29.4252;SVTYPE=BND
MT 16493 gridss9o T T[11:49883585[ 1000 . AS=2;ASQ=201.12915;ASRP=10;ASSR=9;CIGAR=1X239M;CQ=627.96;EVENT=gridss9;MATEID=gridss9h;RAS=1;RASQ=225.70378;REF=7;REFPAIR=2;RP=5;RPQ=86.13501;RSR=1;RSRQ=29.4252;SR=3;SRQ=85.568954;SVTYPE=BND
11 49883585 gridss9h T ]MT:16493]T 1000 . AS=1;ASQ=225.70378;ASRP=10;ASSR=9;BQ=24.57;BSC=1;BSCQ=24.574617;CIGAR=194M1X;CQ=627.96;EVENT=gridss9;MATEID=gridss9o;RAS=2;RASQ=201.12915;REF=9;REFPAIR=6;RP=5;RPQ=86.13501;RSR=3;RSRQ=85.568954;SR=1;SRQ=29.4252;SVTYPE=BND
12 84350 gridss3o G ]12:4886681]G 627.96 . AS=2;ASQ=201.12915;ASRP=10;ASSR=9;CIGAR=1X239M;CQ=627.96;EVENT=gridss3;MATEID=gridss3h;RAS=1;RASQ=225.70378;REF=7;REFPAIR=2;RP=5;RPQ=86.13501;RSR=1;RSRQ=29.4252;SR=3;SRQ=85.568954;SVTYPE=BND
12 4886681 gridss3h T T[12:84350[ 627.96 . AS=1;ASQ=225.70378;ASRP=10;ASSR=9;BQ=24.57;BSC=1;BSCQ=24.574617;CIGAR=194M1X;CQ=627.96;EVENT=gridss3;MATEID=gridss3o;RAS=2;RASQ=201.12915;REF=9;REFPAIR=6;RP=5;RPQ=86.13501;RSR=3;RSRQ=85.568954;SR=1;SRQ=29.4252;SVTYPE=BND
|
