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##fileformat=VCFv4.3
##FILTER=<ID=PASS,Description="All filters passed">
##reference=file://ref.fa
##INFO=<ID=END,Number=1,Type=Integer,Description="End coordinate">
##contig=<ID=1,assembly=b37,length=249250621>
##contig=<ID=2,assembly=b37,length=249250621>
##contig=<ID=3,assembly=b37,length=249250621>
##FILTER=<ID=SnpGap,Description="SNP within 2 bp of mnp,indel,other">
#CHROM POS ID REF ALT QUAL FILTER INFO
1 1000 . G A . PASS .
1 1001 . G A . SnpGap .
1 1003 . GG G . PASS .
1 1006 . G A . SnpGap .
1 1007 . G A . PASS .
2 1000 . G A . PASS .
2 1001 . G A . SnpGap .
2 1003 . G <DEL> . PASS END=1004
2 1006 . G A . SnpGap .
2 1007 . G A . PASS .
3 1000 . G A . PASS .
3 1001 . G A . SnpGap .
3 1003 . GG AA . PASS .
3 1006 . G A . SnpGap .
3 1007 . G A . PASS .
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