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How to convert VCF (with possible predicted gene effects) to protein fasta/MSA

How to convert VCF (with possible predicted gene effects) and multiple samples to protein fasta/MSA

Input:

  • VCF (possibly with already gene/protein effects predicted via e.g. SnpEff)
  • GFF3 (for the reference protein sequence and maybe to predict effects)

Output:

  • protein fasta (1 or 2 sequences per sample in the VCF (2 sequences for heterozygous samples))

Is there any tool that can do this? command line or in python/R code?

gff3 fasta protein vcf
• 2,169 views • link
updated by Emily Emily • written by William William

1 answer

Use the VEP with the ProteinSeqs plugin.

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written by Emily Emily

This only seems to create the protein sequence per variant, not per sample (with possibly multiple variant effects included based on sample genotype(s)).

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written by William William

If you've got phased genotypes then you want Haplosaurus

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written by Emily Emily

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