##fileformat=VCFv4.1
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##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=PARID,Number=1,Type=String,Description="ID of partner breakend">
##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
##ALT=<ID=DUP,Description="">
##ALT=<ID=DEL,Description="">
##ALT=<ID=INV,Description="">
##INFO=<ID=left_chr,Number=1,Type=String,Description="">
##INFO=<ID=left_pos,Number=1,Type=Integer,Description="">
##INFO=<ID=left_strand,Number=1,Type=String,Description="">
##INFO=<ID=left_softclipped_read_count,Number=1,Type=Integer,Description="">
##INFO=<ID=right_chr,Number=1,Type=String,Description="">
##INFO=<ID=right_pos,Number=1,Type=Integer,Description="">
##INFO=<ID=right_strand,Number=1,Type=String,Description="">
##INFO=<ID=right_softclipped_read_count,Number=1,Type=Integer,Description="">
##INFO=<ID=type,Number=1,Type=String,Description="">
##INFO=<ID=left_coverage,Number=1,Type=Integer,Description="">
##INFO=<ID=right_coverage,Number=1,Type=Integer,Description="">
##INFO=<ID=left_assembly_length,Number=1,Type=Integer,Description="assembled length at left_pos">
##INFO=<ID=right_assembly_length,Number=1,Type=Integer,Description="assembled length at right_pos">
##INFO=<ID=left_percent_identity,Number=1,Type=Float,Description="average percent identity at left_pos">
##INFO=<ID=left_percent_multimapping,Number=1,Type=Float,Description="percent of non-unique mapping reads at left_pos">
##INFO=<ID=right_percent_identity,Number=1,Type=Float,Description="average percent identity at right_pos">
##INFO=<ID=right_percent_multimapping,Number=1,Type=Float,Description="percent of non-unique mapping reads at right_pos">
##INFO=<ID=consensus_start_pos,Number=1,Type=Integer,Description="start position of consensus mapping to genome">
##INFO=<ID=consensus_start_chr,Number=1,Type=String,Description="starting chromosome of consensus mapping">
##INFO=<ID=consensus_mapping_start_pos,Number=1,Type=Integer,Description="position of the genomic mapping of consensus starting position">
##INFO=<ID=consensus_mapping_end_pos,Number=1,Type=Integer,Description="end position of consensus mapping to genome">
##INFO=<ID=consensus_end_chr,Number=1,Type=String,Description="ending chromsome of consnesus mapping">
##INFO=<ID=consensus_mapping_end_pos2,Number=1,Type=Integer,Description="position of genomic mapping of consensus ending posiiton">
##INFO=<ID=consensus,Number=1,Type=String,Description="consensus sequences">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
chr7	205219	line1	N	<DUP>	.	PASS	SVTYPE=DUP;SVLEN=177;left_chr=chr7;left_pos=205396;left_strand=+;left_softclipped_read_count=7;right_chr=chr7;right_pos=205219;right_strand=+;right_softclipped_read_count=9;left_coverage=60;right_coverage=59;left_assembly_length=34;right_assembly_length=34;left_percent_identity=0.833608360836;left_percent_multimapping=0.208333333333;right_percent_identity=0.774901586544;right_percent_multimapping=0.313253012048;consensus_start_pos=1;consensus_start_chr=chr7;consensus_mapping_start_pos=205266;consensus_mapping_end_pos=205293;consensus_end_chr=chr7;consensus_mapping_end_pos2=205293;consensus=AGCCCCCCGAGTAGCCGGGACCACGGACACGCACCGCCACGACGTCAGCCCCCCGAGTAGCCGGGACCACGGACACGCACCGCCACGACGTCAGCCCCCCGAGTAGCCGGGACCACGGAC
chr7	1185078	line2	N	<DEL>	.	PASS	SVTYPE=DEL;SVLEN=2577;left_chr=chr7;left_pos=1185078;left_strand=+;left_softclipped_read_count=13;right_chr=chr7;right_pos=1187655;right_strand=+;right_softclipped_read_count=15;left_coverage=45;right_coverage=35;left_assembly_length=77;right_assembly_length=67;left_percent_identity=0.750619909232;left_percent_multimapping=0.527777777778;right_percent_identity=0.692766562364;right_percent_multimapping=0.690909090909;consensus_start_pos=1;consensus_start_chr=chr7;consensus_mapping_start_pos=1184985;consensus_mapping_end_pos=1187745;consensus_end_chr=chr7;consensus_mapping_end_pos2=1187745;consensus=ACTTCTGGGTTCAAGTGATCCACCCGCCTTGGCCCCCCCAAAGTTTTGGTCTTACAGGCCTGAGCCACCACACCTGGCCTCACTCTTAAGTTTTATACTTCAATACTCCGTCAAATCGAAGACAGAAAACGCAATGCATGAACCAGGCGCCGCCTCTCCCCGCTGAGAAAA
chr1	242143860	line3o	N	N[chr7:1623213[	.	PASS	SVTYPE=BND;PARID=line3h;EVENT=CTXline3
chr7	1623213	line3h	N	]chr1:242143860]N	.	PASS	SVTYPE=BND;PARID=line3o;EVENT=CTXline3;left_chr=chr1;left_pos=242143860;left_strand=+;left_softclipped_read_count=12;right_chr=chr7;right_pos=1623213;right_strand=+;right_softclipped_read_count=6;left_coverage=49;right_coverage=52;left_assembly_length=75;right_assembly_length=73;left_percent_identity=0.929409607627;left_percent_multimapping=0.111111111111;right_percent_identity=0.869106820184;right_percent_multimapping=0.288461538462;consensus_start_pos=1;consensus_start_chr=chr1;consensus_mapping_start_pos=242143767;consensus_mapping_end_pos=1623297;consensus_end_chr=chr7;consensus_mapping_end_pos2=1623297;consensus=CATGCTACAGACACAAGGTGCCAGATGAACTTGAGGATAGTCCTTAAACACAAATAAAATCTGTCTGTAGCTTTGGCATTAGAAGTAGAGTCCCGGTCAAGAGTTTGAGACCAGCCTGACCAACATGGTGAAACCCTGTCTCTACTAAAAACAAAACAAAAAAAATTAGCTGGACATGG
chr7	40879375	line46	N	<INV>	.	PASS	SVTYPE=INV;SVLEN=1095;left_chr=chr7;left_pos=40879375;left_strand=+;left_softclipped_read_count=8;right_chr=chr7;right_pos=40880470;right_strand=-;right_softclipped_read_count=13;left_coverage=37;right_coverage=52;left_assembly_length=55;right_assembly_length=67;left_percent_identity=0.813936110592;left_percent_multimapping=0.471698113208;right_percent_identity=0.862068965517;right_percent_multimapping=0.396551724138;consensus_start_pos=1;consensus_start_chr=chr7;consensus_mapping_start_pos=40879286;consensus_mapping_end_pos=40880403;consensus_end_chr=chr7;consensus_mapping_end_pos2=40880403;consensus=GTAAACTTTTAATGACTGCAGGATCTGGAGTGATGTCCCTTGTTTCATTCTTGATATTTGTAATTTATGTTTTCTCTATTTTTATTTTGTCAGACTTAGCAGGAGTTATTTGATATTTGTAATTTATGTTTTCTCTATTTTTATTTTGTCAGACTTAGC
