I've performed variant calling with two callers. One calls haplotypes and other calls mutations as single variants. As a result I have two VCF files where sometimes identical variants are written in different forms. For example: One file:
chr1 61987 . AAG GAC
chr1 61987 . A G chr1 61989 . G C
Obviously, mutations in the second file are from single haplotype and in the final VCF file i need only single record as in the first file. I've tried to use bcftools merge to combine VCF files, but I get the following:
chr1 61987 . AAG GAC,GAG
Which will lead to wrong annotation. So is there any software to combine these two VCF files into single one, so all single variants would disappear?