gatk-3.8/public/testdata/breakpoint-example.vcf

##fileformat=VCFv4.1
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
22	50	bnd_W	G	G]22:6000]	6	PASS	SVTYPE=BND;MATEID=bnd_Y
22	51	bnd_V	T	]22:55]T	6	PASS 	SVTYPE=BND;MATEID=bnd_U
22	55	bnd_U	C	C[22:51[	6	PASS 	SVTYPE=BND;MATEID=bnd_V
22	6000	bnd_Y	A	A]22:50]	6	PASS 	SVTYPE=BND;MATEID=bnd_W
Added support for breakpoint alleles -- See https://getsatisfaction.com/gsa/topics/support_vcf_4_1_structural_variation_breakend_alleles?utm_content=topic_link&utm_medium=email&utm_source=new_topic -- Added integrationtest to ensure that we can parse and write out breakpoint example 2012-02-24 01:14:48 +08:00			`##fileformat=VCFv4.1`
			`#CHROM POS ID REF ALT QUAL FILTER INFO`
			`22 50 bnd_W G G]22:6000] 6 PASS SVTYPE=BND;MATEID=bnd_Y`
			`22 51 bnd_V T ]22:55]T 6 PASS SVTYPE=BND;MATEID=bnd_U`
			`22 55 bnd_U C C[22:51[ 6 PASS SVTYPE=BND;MATEID=bnd_V`
			`22 6000 bnd_Y A A]22:50] 6 PASS SVTYPE=BND;MATEID=bnd_W`