Entering edit mode
5.9 years ago
Hi,
I saw that VEP provides a 'transcript_consequences' annotation with 'cds_start' and 'cds_end' fields. But they do not indicate the amino acids length. Is there a way to get the amino acids length from the annotations? I haven't seen any possible field in the annotations structure:
"transcript_consequences": [
{
"variant_allele": "G",
"consequence_terms": [
"missense_variant"
],
"gene_id": "ENSG00000135744",
"gene_symbol": "AGT",
"gene_symbol_source": "HGNC",
"transcript_id": "ENST00000366667",
"biotype": "protein_coding",
"strand": -1,
"cdna_start": 1018,
"cdna_end": 1018,
"cds_start": 803,
"cds_end": 803,
"protein_start": 268,
"protein_end": 268,
"codons": "aTg/aCg",
"amino_acids": "M/T",
"polyphen_prediction": "benign",
"polyphen_score": 0,
"sift_prediction": "tolerated",
"sift_score": 1,
"hgvsc": "ENST00000366667.4:c.803T>C",
"hgvsp": "ENSP00000355627.4:p.Met268Thr"
}
Thanks.
Ok, thanks for the very fast reply!