Tool that can merge 2 VCF files while taking “representational ambiguity” of (multi-allelic) variants into account

Tool that can merge 2 VCF files while taking “representational ambiguity” of (multi-allelic) variants into account

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Is there a tool that can merge 2 VCF files while taking “representational ambiguity” of multi-allelic variants into account?

By:

  • replaying all variant alleles from the 2 VCF files into the reference genome
  • identifying which alleles are actually the same but just written down in a different way
  • calculating what the best way is to represent the merged variants/alleles in a new (multi-allelic) variant

See also this question and answer.
Should you decompose and normalize multi-allelic variants for comparison / ID assignment?

The (multi-allelic) variants (alleles) in both VCF files are different because:

  1. different technology used to make the VCF files
  2. different alternative alleles present in samples

BCFtools merge does not take “representational ambiguity” of variants into account (as far as I know)

First decomposing and normalizing all variants to bi-allelic in both input VCF files, then merging and collapsing overlapping variants back to multi-allelic destroys some information?


vcf


merge


bcftools


multi-allelic

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