##fileformat=VCFv4.1
##fileDate=20170804
##source=GenerateSVCandidates 1.1.1
##reference=file:///home/users/allstaff/cameron.d/reference_genomes/human_new/no_alt/hg38_no_alt.fa
##contig=<ID=chr1,length=248956422>
##contig=<ID=chr2,length=242193529>
##contig=<ID=chr3,length=198295559>
##contig=<ID=chr4,length=190214555>
##contig=<ID=chr5,length=181538259>
##contig=<ID=chr6,length=170805979>
##contig=<ID=chr7,length=159345973>
##contig=<ID=chr8,length=145138636>
##contig=<ID=chr9,length=138394717>
##contig=<ID=chr10,length=133797422>
##contig=<ID=chr11,length=135086622>
##contig=<ID=chr12,length=133275309>
##contig=<ID=chr13,length=114364328>
##contig=<ID=chr14,length=107043718>
##contig=<ID=chr15,length=101991189>
##contig=<ID=chr16,length=90338345>
##contig=<ID=chr17,length=83257441>
##contig=<ID=chr18,length=80373285>
##contig=<ID=chr19,length=58617616>
##contig=<ID=chr20,length=64444167>
##contig=<ID=chr21,length=46709983>
##contig=<ID=chr22,length=50818468>
##contig=<ID=chrX,length=156040895>
##contig=<ID=chrY,length=57227415>
##contig=<ID=chrM,length=16569>
##cmdline=/wehisan/bioinf/bioinf-data/Papenfuss_lab/projects/sv_benchmark/scripts/tools/manta/1.1.1/bin/configManta.py --bam input.bam --referenceFasta /home/users/allstaff/cameron.d/reference_genomes/human_new/no_alt/hg38_no_alt.fa --runDir /wehisan/bioinf/bioinf-data/Papenfuss_lab/projects/sv_benchmark/scripts/../data.chm/16c58fbcc5633564b10ebe8f78d87883
##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	/wehisan/bioinf/bioinf-data/Papenfuss_lab/projects/sv_benchmark/scripts/../data.chm/chm1.1.fq
chr1	1570957	MantaBND:103:0:1:0:0:0:0	A	]chr15:93292550]A	260	PASS	SVTYPE=BND;MATEID=MantaBND:103:0:1:0:0:0:1;CIPOS=0,7;HOMLEN=7;HOMSEQ=AAAATTT;BND_DEPTH=58;MATE_BND_DEPTH=41	GT:FT:GQ:PL:PR:SR	0/1:PASS:260:310,0,999:16,1:30,10
chr1	1605661	MantaDEL:1:45:45:2:2:0	TGTGGGGTCGGCTGGTCAGGTGTGGGCTGGGCTGGTCAGGTGTGGGGTGGGCTGGTCAGGTGTGGGCTGGGCTGGTCAGGTGTGGGCTGGGCTGGTCAGGTGTGCGGTGGGCTGGGCTGGTCAGGTGTGGGCTGGGCTGGTCAGGTGTGGGGTCGGATGGTCAGGC	T	208	PASS	END=1605826;SVTYPE=DEL;SVLEN=-165;CIGAR=1M165D;CIPOS=0,5;HOMLEN=5;HOMSEQ=GTGGG	GT:FT:GQ:PL:PR:SR	0/1:PASS:208:258,0,941:20,0:44,17
chr1	1929384	MantaINS:1:50:50:0:5:0	G	<INS>	400	MinGQ	END=1929384;SVTYPE=INS;CIPOS=0,5;CIEND=0,5;HOMLEN=5;HOMSEQ=GAGGG;LEFT_SVINSSEQ=GAGGGGACAGGTCTGGGGAGGCAGGAGAGAGGGTGAGGGGAGGCAGGGGAGAGGGTGAGGGGAGGGAGGGGAGAGGGTGGGGGAGGGAGG;RIGHT_SVINSSEQ=AGAGGGTAGGGAGGGAGGGCAGGAGGGGAGAGGGTAGGGAGGGAGGGGAGGAAGGGAGAGGGTAGGGAGGGGAGGAGGGGAGAGGGTAGGGAGGGAGGGAGAGGAGGGGA	GT:FT:GQ:PL:PR:SR	1/1:MinGQ:10:453,12,0:0,0:0,19
chr1	11431744	MantaINV:746:0:2:0:0:0	C	<INV>	227	NoPairSupport	END=118852083;SVTYPE=INV;SVLEN=107420339;CIPOS=0,18;CIEND=-18,0;HOMLEN=18;HOMSEQ=TTTCTTTCTTTCTTTCTT;INV3	GT:FT:GQ:PL:PR:SR	0/1:PASS:227:277,0,462:12,0:10,11
chr1	12138948	MantaDUP:TANDEM:798:0:1:0:0:0	G	<DUP:TANDEM>	44	PASS	END=12139014;SVTYPE=DUP;SVLEN=66;CIPOS=0,2;CIEND=0,2;HOMLEN=2;HOMSEQ=CT	GT:FT:GQ:PL:PR:SR	0/1:PASS:44:94,0,999:9,2:33,8
chr2	48244349	MantaINS:14002:0:0:0:0:0	TCTTC	TTTTTTTTTTTTTTTTTTTTT	candidateSmallIndels	.	END=48244353;SVTYPE=INS;SVLEN=20;CIGAR=1M20I4D;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0
chr2	48260892	MantaDEL:13943:0:0:0:0:0	CTTCTCCCA	C	candidateSmallIndels	.	END=48260900;SVTYPE=DEL;SVLEN=-8;CIGAR=1M8D;CIPOS=0,16;HOMLEN=16;HOMSEQ=TTCTCCCATTCTCCCA;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0
chr15	93292550	MantaBND:103:0:1:0:0:0:1	C	C[chr1:1570957[	260	PASS	SVTYPE=BND;MATEID=MantaBND:103:0:1:0:0:0:0;CIPOS=0,7;HOMLEN=7;HOMSEQ=AAAAATT;BND_DEPTH=41;MATE_BND_DEPTH=58	GT:FT:GQ:PL:PR:SR	0/1:PASS:260:310,0,999:16,1:30,10
chr16	57595220	MantaINS:119539:0:0:0:0:0	G	GTTTTTTTTTTTT	candidateSV	.	END=57595220;SVTYPE=INS;SVLEN=12;CIGAR=1M12I;CIPOS=0,16;HOMLEN=16;HOMSEQ=TTTTTTTTTTTTTTTT;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0
chr16	57691483	MantaDEL:119560:0:1:0:0:0	G	<DEL>	candidateSV	.	END=57693934;SVTYPE=DEL;SVLEN=-2451;UPSTREAM_PAIR_COUNT=3;DOWNSTREAM_PAIR_COUNT=3;PAIR_COUNT=3
chr16	59050064	MantaDUP:TANDEM:83323:1:1:1:0:0	C	<DUP:TANDEM>	candidateSV	.	END=59050093;SVTYPE=DUP;SVLEN=29;CIPOS=0,1;CIEND=0,1;HOMLEN=1;HOMSEQ=G;UPSTREAM_PAIR_COUNT=0;DOWNSTREAM_PAIR_COUNT=0;PAIR_COUNT=0
