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
Another file:
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?
•
written
by
Max Ivon
1 answer
A solution with the GATK (pre-4.0): LeftAlignAndTrimVariants. You can split or combine multiallelic records with bcftools norm.
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