VEP output is only protein_coding

VEP output is only protein_coding

1

Hello,
I am supposed to extract both protein coding and synonymous variants from VCFs that were given to me. Only variant consequence i find here is “Protein_coding”, but no strings as “synonymous” are present there. Is that some error with VEP?

Thank you!


VEP

• 57 views

Hi, Protein_coding is not exactly a consequence – it just provides information about the location of the variant with respect to a given transcript isoform.

I think that you may want to think about the definition of ‘synonymous‘:

  • synonymous base substitution (synonymous variant / synonymous
    mutation): a base change in a protein coding region that does not
    alter the resulting amino acid sequence
  • non-synonymous base substitution (non-synonymous variant / non-synonymous
    mutation): a base change in a protein coding region that does [yes] alter the resulting amino acid sequence

If you wish, please show the command that you used to annotate the variants, and also show a sample of the output that was produced.

Kevin


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