##fileformat=VCFv4.2
##reference=/home/cog/jvalleinclan/kloosterman/tools/longranger-2.2.2/refdata-b37-2.1.0/fasta/genome.fa
##phasing=none
##source=10X/pipelines/stages/analyze_sv_calls 2.2.2
##INFO=<ID=END,Number=1,Type=Integer,Description="Confidence interval around END for imprecise variants">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
##INFO=<ID=IMPRECISE_DIR,Number=0,Type=Flag,Description="Imprecise orientation of breakend">
##INFO=<ID=POS,Number=1,Type=Integer,Description="Start position of the variant described in this record">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=SVTYPE2,Number=1,Type=String,Description="Type of structural variant implied by breakends">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=PS,Number=1,Type=Integer,Description="Phase set assignment">
##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
##INFO=<ID=HAP_ALLELIC_FRAC,Number=1,Type=Float,Description="Haplotype allelic fraction">
##INFO=<ID=ALLELIC_FRAC,Number=1,Type=Float,Description="Allelic fraction">
##INFO=<ID=PAIRS,Number=1,Type=Integer,Description="Number of supporting read pairs">
##INFO=<ID=SPLIT,Number=1,Type=Integer,Description="Number of supporting split reads">
##INFO=<ID=WildCov,Number=1,Type=Float,Description="Number of barcodes in the wild haplotype">
##INFO=<ID=MolTtl,Number=1,Type=Integer,Description="Total number of barcodes in the region of the deletion">
##INFO=<ID=MolTtlNoR,Number=1,Type=Integer,Description="Number of barcodes without covering reads in the region of the deletion">
##INFO=<ID=MolDel,Number=1,Type=Integer,Description="Total number of barcodes in deleted haplotype">
##INFO=<ID=MolDelNoR,Number=1,Type=Integer,Description="Number of barcodes without covering reads in deleted haplotype">
##INFO=<ID=MolWild,Number=1,Type=Integer,Description="Total number of barcodes in wild haplotype">
##INFO=<ID=MolWildNoR,Number=1,Type=Integer,Description="Number of barcodes without covering reads in wild haplotype">
##INFO=<ID=PVAL,Number=1,Type=Float,Description="p-value for the called event">
##INFO=<ID=BGSize,Number=1,Type=Integer,Description="Size of the background region">
##INFO=<ID=BGImparityPval,Number=1,Type=Float,Description="The p-value for the hypothesis that the two haplotypes in the background region have different barcode coverage">
##INFO=<ID=BGTtlRCnt,Number=1,Type=Integer,Description="Total number of barcodes in the background region">
##INFO=<ID=BGHP1RCnt,Number=1,Type=Integer,Description="Number of barcodes on haplotype 1 in the background region">
##INFO=<ID=BGHP2RCnt,Number=1,Type=Integer,Description="Number of barcodes on haplotype 2 in the background region">
##INFO=<ID=BGBaseCov,Number=1,Type=Float,Description="Base level coverage in the background region">
##INFO=<ID=BGPhaseFrac,Number=1,Type=Float,Description="Fraction of reads phased">
##INFO=<ID=NRead,Number=1,Type=Float,Description="Number of barcodes covering the homo deletion region">
##INFO=<ID=SOURCE,Number=1,Type=String,Description="Method from which the event is called">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FILTER=<ID=BLACK_DIST,Description="Too close to the SV blacklist">
##FILTER=<ID=BLACK_FRAC,Description="Too much overlap with the SV blacklist">
##FILTER=<ID=SEG_DUP,Description="Breakpoints overlap copies of the same segmental duplication">
##FILTER=<ID=LOWQ,Description="Low confidence call">
##FILTER=<ID=LARGE_PVALUE,Description="Insignificant pvalue">
##FILTER=<ID=LOW_WILD_COV,Description="Too few reads on the wild type haplotype and hence an unliable pvalue calculation">
##FILTER=<ID=IMPARITY_IN_HAP_COV,Description="In the background region, one haplotype has significanlty more reads than the other haplotype">
##FILTER=<ID=LOW_COV_REGION,Description="The background region has significantly low barcode coverage">
##FILTER=<ID=LOW_PHASING_REGION,Description="Low fraction of reads phased in the background region">
##FILTER=<ID=CNV_SEG_DUP,Description="Called events overlap with segdup tracks with sequence identity is 98% or higher">
##FILTER=<ID=LowCov,Description="Called events overlap with low exome target regions">
##FILTER=<ID=HighContamination,Description="Too many potential contaminated barcodes in a supposedly homo deletion region">
##ALT=<ID=UNK,Description="SV of unknown type">
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=DUP:TANDEM,Description="Tandem Duplication">
##ALT=<ID=INV,Description="Inversion">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	COLO829T_somatic_10X
1	0	call_203	N	<DEL>	370	PASS	END=650000;CIEND=0,0;CIPOS=0,0;SVTYPE=DEL;SVLEN=-650000;PS=.;HAP_ALLELIC_FRAC=.;ALLELIC_FRAC=.;PAIRS=.;SPLIT=.;WildCov=.;MolTtl=.;MolTtlNoR=.;MolDel=.;MolDelNoR=.;MolWild=.;MolWildNoR=.;PVAL=.;BGSize=.;BGImparityPval=.;BGTtlRCnt=.;BGHP1RCnt=.;BGHP2RCnt=.;BGBaseCov=.;BGPhaseFrac=.;NRead=.;SOURCE=CNV	GT	0/1
1	1594880	call_2416_1	A	[1:1660850[A	3	BLACK_FRAC;LOWQ;SEG_DUP	CIPOS=-6,6;IMPRECISE_DIR;SVTYPE=BND;SVTYPE2=BND;PS=978943;MATEID=call_2416_2;EVENT=call_2416;HAP_ALLELIC_FRAC=0.75;ALLELIC_FRAC=0.0212765957447;PAIRS=3;SPLIT=0;WildCov=.;MolTtl=.;MolTtlNoR=.;MolDel=.;MolDelNoR=.;MolWild=.;MolWildNoR=.;PVAL=.;BGSize=.;BGImparityPval=.;BGTtlRCnt=.;BGHP1RCnt=.;BGHP2RCnt=.;BGBaseCov=.;BGPhaseFrac=.;NRead=.;SOURCE=SV	GT	1|0
1	1660850	call_2416_2	T	[1:1594880[T	3	BLACK_FRAC;LOWQ;SEG_DUP	CIPOS=-6,6;IMPRECISE_DIR;SVTYPE=BND;SVTYPE2=BND;PS=1654098;MATEID=call_2416_1;EVENT=call_2416;HAP_ALLELIC_FRAC=0.75;ALLELIC_FRAC=0.0212765957447;PAIRS=3;SPLIT=0;WildCov=.;MolTtl=.;MolTtlNoR=.;MolDel=.;MolDelNoR=.;MolWild=.;MolWildNoR=.;PVAL=.;BGSize=.;BGImparityPval=.;BGTtlRCnt=.;BGHP1RCnt=.;BGHP2RCnt=.;BGBaseCov=.;BGPhaseFrac=.;NRead=.;SOURCE=SV	GT	1|0
1	2632545	call_534	G	<UNK>	30	BLACK_DIST;BLACK_FRAC;SEG_DUP	END=2689665;CIEND=-10,11;CIPOS=-10,11;SVTYPE=UNK;SVLEN=57120;PS=2614362;HAP_ALLELIC_FRAC=0.967741935484;ALLELIC_FRAC=0.526315789474;PAIRS=2;SPLIT=0;WildCov=.;MolTtl=.;MolTtlNoR=.;MolDel=.;MolDelNoR=.;MolWild=.;MolWildNoR=.;PVAL=.;BGSize=.;BGImparityPval=.;BGTtlRCnt=.;BGHP1RCnt=.;BGHP2RCnt=.;BGBaseCov=.;BGPhaseFrac=.;NRead=.;SOURCE=SV	GT	0|1
1	12998613	call_2420	T	<INV>	3	BLACK_DIST;BLACK_FRAC;LOWQ	END=13052761;CIEND=0,1;CIPOS=0,1;SVTYPE=INV;SVLEN=54148;PS=12990340;HAP_ALLELIC_FRAC=0.25;ALLELIC_FRAC=0.0454545454545;PAIRS=.;SPLIT=.;WildCov=.;MolTtl=.;MolTtlNoR=.;MolDel=.;MolDelNoR=.;MolWild=.;MolWildNoR=.;PVAL=.;BGSize=.;BGImparityPval=.;BGTtlRCnt=.;BGHP1RCnt=.;BGHP2RCnt=.;BGBaseCov=.;BGPhaseFrac=.;NRead=.;SOURCE=SV	GT	1|0
1	14952581	call_2422	T	<DUP:TANDEM>	3	LOWQ	END=14999607;CIEND=0,1;CIPOS=0,1;SVTYPE=DUP;SVLEN=47026;PS=13583731;HAP_ALLELIC_FRAC=0.3;ALLELIC_FRAC=0.01246105919;PAIRS=.;SPLIT=.;WildCov=.;MolTtl=.;MolTtlNoR=.;MolDel=.;MolDelNoR=.;MolWild=.;MolWildNoR=.;PVAL=.;BGSize=.;BGImparityPval=.;BGTtlRCnt=.;BGHP1RCnt=.;BGHP2RCnt=.;BGBaseCov=.;BGPhaseFrac=.;NRead=.;SOURCE=SV	GT	0|1