VEP output is only protein_coding
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!
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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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