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  • Resolve indel genotype alleles

    Is there a tool that can resolve by-sample indel genotypes from multiple samples to a multi-allelic VCF locus record?

    Simple example of by-sample genotypes:

    #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1
    1 5 . ACG A . . . GT 0/1

    #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample2
    1 6 . CG C . . . GT 0/1

    Looking for a method that would resolve to this:

    #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
    1 5 . ACG A,AC . . . GT 0/1 0/2

  • #2
    Have you tried GATK CombineVariants walker?

    Comment


    • #3
      Yes, as expected from the description (CombineVariants will include a record at every site in all of your input VCF file), it appears to be using #CHROM POS as a key to define "site" and thus does not attempt to combine these two variants.

      Comment

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