##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##reference=file:///some/path/1000GenomesPilot-NCBI36.fasta
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=1,length=2147483647>
##INFO=<ID=FIXREF,Number=.,Type=String,Description="The change made by bcftools/fixref">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	XY00001
1	1	rs1	C	T	.	.	FIXREF=none	GT	0/1
1	2	rs2	A	T	.	.	FIXREF=skip	GT	1/0
1	3	rs3	A	T	.	.	FIXREF=skip	GT	0/1
1	4	rs4	T	A	.	.	FIXREF=skip	GT	1/0
1	5	rs5	C	T	.	.	FIXREF=none	GT	0/1
1	6	rs6	C	T	.	.	FIXREF=swap,GT	GT	0/1
