##fileformat=VCFv4.1
##fileDate=20160521
##source=GenerateSVCandidates 0.29.6
##reference=file:///home/users/allstaff/cameron.d/reference_genomes/human/hg19.fa
##contig=<ID=chr1,length=249250621>
##contig=<ID=chr10,length=135534747>
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##contig=<ID=chr11_gl000202_random,length=40103>
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##contig=<ID=chrM,length=16571>
##contig=<ID=chrUn_gl000211,length=166566>
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##contig=<ID=chrX,length=155270560>
##contig=<ID=chrY,length=59373566>
##cmdline=/wehisan/bioinf/bioinf-data/Papenfuss_lab/projects/sv_benchmark/tools/manta/0.29.6/bin/configManta.py --bam input.bam --referenceFasta /home/users/allstaff/cameron.d/reference_genomes/human/hg19.fa --runDir /wehisan/bioinf/bioinf-data/Papenfuss_lab/projects/sv_benchmark/data.na12878/51e19d10ab3ccadcda339e8da2bc593e
##FILTER=<ID=candidateSV,Description="Variant output to candidateSV call set">
##FILTER=<ID=candidateSmallIndels,Description="Variant output to candidateSmallIndels call set">
##ALT=<ID=BND,Description="Translocation Breakend">
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=DUP:TANDEM,Description="Tandem Duplication">
##ALT=<ID=INS,Description="Insertion">
##ALT=<ID=INV,Description="Inversion">
##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=MinGQ,Description="GQ score is less than 15 (filter applied at sample level and record level if all samples are filtered)">
##FILTER=<ID=MinQUAL,Description="QUAL score is less than 20">
##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=Ploidy,Description="For DEL & DUP variants, the genotypes of overlapping variants (with similar size) are inconsistent with diploid expectation">
##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=Float,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##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">
##INFO=<ID=BND_DEPTH,Number=1,Type=Integer,Description="Read depth at local translocation breakend">
##INFO=<ID=BND_PAIR_COUNT,Number=1,Type=Integer,Description="Confidently mapped reads supporting this variant at this breakend (mapping may not be confident at remote breakend)">
##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=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS">
##INFO=<ID=DOWNSTREAM_PAIR_COUNT,Number=1,Type=Integer,Description="Confidently mapped reads supporting this variant at this downstream breakend (mapping may not be confident at upstream breakend)">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##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=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=INV3,Number=0,Type=Flag,Description="Inversion breakends open 3' of reported location">
##INFO=<ID=INV5,Number=0,Type=Flag,Description="Inversion breakends open 5' of reported location">
##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">
##INFO=<ID=LEFT_SVINSSEQ,Number=.,Type=String,Description="Known left side of insertion for an insertion of unknown length">
##INFO=<ID=MATE_BND_DEPTH,Number=1,Type=Integer,Description="Read depth at remote translocation mate breakend">
##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakend">
##INFO=<ID=PAIR_COUNT,Number=1,Type=Integer,Description="Read pairs supporting this variant where both reads are confidently mapped">
##INFO=<ID=RIGHT_SVINSSEQ,Number=.,Type=String,Description="Known right side of insertion for an insertion of unknown length">
##INFO=<ID=SVINSLEN,Number=.,Type=Integer,Description="Length of insertion">
##INFO=<ID=SVINSSEQ,Number=.,Type=String,Description="Sequence of insertion">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=UPSTREAM_PAIR_COUNT,Number=1,Type=Integer,Description="Confidently mapped reads supporting this variant at the upstream breakend (mapping may not be confident at downstream breakend)">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	garvan
chr1	822799	MantaBND:56:0:1:0:2:0:0	C	]chr9:141088189]C	999	MaxDepth	SVTYPE=BND;MATEID=MantaBND:56:0:1:0:2:0:1;BND_DEPTH=201;MATE_BND_DEPTH=145	GT:FT:GQ:PL:PR:SR	0/1:PASS:999:999,0,999:218,5:81,71
chr9	141088189	MantaBND:56:0:1:0:2:0:1	A	A[chr1:822799[	999	MaxDepth	SVTYPE=BND;MATEID=MantaBND:56:0:1:0:2:0:0;BND_DEPTH=145;MATE_BND_DEPTH=201	GT:FT:GQ:PL:PR:SR	0/1:PASS:999:999,0,999:218,5:81,71
chr1	822799	MantaBND:56:0:1:0:2:0:0	C	]chr9:141088189]C	candidateSV	.	SVTYPE=BND;MATEID=MantaBND:56:0:1:0:2:0:1;BND_PAIR_COUNT=5;PAIR_COUNT=5
chr9	141088189	MantaBND:56:0:1:0:2:0:1	A	A[chr1:822799[	candidateSV	.	SVTYPE=BND;MATEID=MantaBND:56:0:1:0:2:0:0;BND_PAIR_COUNT=5;PAIR_COUNT=5
chr1	6618972	MantaINS:549:0:0:0:0:0	GAT	GTACTAGGATTACAGGCGTGAACCACCTCGCCTGGCCAAAACCTCAGGCTTTTTTTTTTTTTTTGAGAG	284	PASS	END=6618974;SVTYPE=INS;SVLEN=68;CIGAR=1M68I2D	GT:FT:GQ:PL:PR:SR	0/1:PASS:284:334,0,361:0,0:11,18
chr1	5559500	MantaDEL:449:0:0:0:0:1	AGATAGATAATAGGTCTAGATAGATGATAGATAGATAGATAGAAGATAGATAGATGACAGATAGATGATAGATATATAGTAGATAGAAGATAGATAGATAGATAGAT	A	448	PASS	END=5559606;SVTYPE=DEL;SVLEN=-106;CIGAR=1M106D;CIPOS=0,8;HOMLEN=8;HOMSEQ=GATAGATA	GT:FT:GQ:PL:PR:SR	0/1:PASS:448:498,0,999:16,3:22,12
chr1	755801	MantaDEL:2:0:0:0:0:1	CCTGTCTACACTACCTGCCTGGTCAGTATATCCACCCTATCTACACTACCTGCCTGGCCAGCATATCCGCCCTGTCTACACTACCTCCCAGCCCAGCAGATCCGCCCTGTCTACACTACCTGCCTGGCCAGTAGATCCACG	C	114	PASS	END=755941;SVTYPE=DEL;SVLEN=-140;CIGAR=1M140D;CIPOS=0,2;HOMLEN=2;HOMSEQ=CT	GT:FT:GQ:PL:PR:SR	0/1:PASS:114:164,0,999:60,2:87,9
chr1	755801	MantaDEL:2:0:0:0:0:1	CCTGTCTACACTACCTGCCTGGTCAGTATATCCACCCTATCTACACTACCTGCCTGGCCAGCATATCCGCCCTGTCTACACTACCTCCCAGCCCAGCAGATCCGCCCTGTCTACACTACCTGCCTGGCCAGTAGATCCACG	C	candidateSV	.	END=755941;SVTYPE=DEL;SVLEN=-140;CIGAR=1M140D;CIPOS=0,2;HOMLEN=2;HOMSEQ=CT;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0		
