Instead of specifying genomic variants (whose protein effect is predicted) you can now instead use --protein-change GENE-NAME <change>. This currently only works for amino acid substitutions (in a format like "T790M") and not for other kinds of mutations. Another limitations is that the gene names must match what's used in Ensembl, other gene synonyms will not work.
Internally the protein change strings are parsed into Varcode effects (whose variant field is None). The transcript for each protein change is selected by filtering to coding transcripts whose amino acid sequence matches the reference amino acids from the change descriptor. If multiple matching transcripts exist, then the longest is chosen.
Instead of specifying genomic variants (whose protein effect is predicted) you can now instead use
--protein-change GENE-NAME <change>. This currently only works for amino acid substitutions (in a format like "T790M") and not for other kinds of mutations. Another limitations is that the gene names must match what's used in Ensembl, other gene synonyms will not work.Internally the protein change strings are parsed into Varcode effects (whose
variantfield isNone). The transcript for each protein change is selected by filtering to coding transcripts whose amino acid sequence matches the reference amino acids from the change descriptor. If multiple matching transcripts exist, then the longest is chosen.