I am attempting to insert observed variant modifications from Annovar, into protein sequences that I have retrieved from the UCSC file knownGeneTxPep. Variant positions from the start of a transcript were retrieved from Annovar. Here is my question:
When I make a mapping from peptide id (say uc010nwy.3) to transcript ID (say NM_0010757) using "kgXref" there is not a 1:1 mapping. There are more peptide ids than transcript ids, meaning multiple tsids map to a peptide ID. This confounds what I am trying to do because I don't know which peptide sequence to alter when annovar says that a variant was observed in transcript X.
I'm not certain I'm using the correct files for the task and I've been unable to find any documentation. Any help would be great.