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

Question

[William]

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?

Answer 1

[Emily]

Use the VEP with the ProteinSeqs plugin.

[William]

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

[Emily]

If you've got phased genotypes then you want Haplosaurus