I have a vcf with multi-allelic SNPs, e.g. REF: A and ALT: G, C.

I would like to combine all reference alleles to the most frequent reference alleles. This should reflect both in the REF field and in the genotypes themselves.

Can this be done with an existing tool?

  • $\begingroup$ Please edit your question and add a few lines from a VCF file that we can use to reproduce your issue. Make sure to also show us the output you expect from those lines. $\endgroup$
    – terdon
    Oct 15 at 9:42
  • $\begingroup$ I would suggest computing the population frequencies of each allele, using suggestions here: biostars.org/p/366694. You will then have the frequencies of each allele, you can make up your own mind which alleles to combine. $\endgroup$ Oct 18 at 16:21

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