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##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 T A . . FIXREF=swap,GT GT 0/1
1 3 rs3 A T . . FIXREF=none GT 0/1
1 4 rs4 A T . . FIXREF=swap,GT GT 0/1
1 5 rs5 C T . . FIXREF=none GT 0/1
1 6 rs6 C T . . FIXREF=swap,GT GT 0/1
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