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##fileformat=VCFv4.2
##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=MATEID,Number=.,Type=String,Description="ID of mate breakends">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant">
##ALT=<ID=DEL,Description="Deletion">
##contig=<ID=chr,length=18,sequence="CGTGTtgtagtaCCGTAA">
#CHROM POS ID REF ALT QUAL FILTER INFO
chr 5 sequence TTGTAGTA T . .
chr 5 symbolic T <DEL> . . SVTYPE=DEL;SVLEN=-7;END=12
chr 5 breakpoint1 T T[chr:13[ . . SVTYPE=BND;MATEID=breakpoint2
chr 13 breakpoint2 C ]chr:5]C . . SVTYPE=BND;MATEID=breakpoint1
chr 5 breakend T T. . . SVTYPE=BND
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