based on a recent annotation of resulted vcf files regarding the identification of somatic point alterations in a specific cancer of interest, I used ANNOVAR default settings with gencode annotation. Based on the relative output of files, I noticed the following pattern in a specific column (ANNOVAR_TRANSCRIPTS) regarding multiple variant transcripts for each variant/specific gene, for example:
However, this poses a general problem in which of the transcripts to select/consider as the “main transcript variant”, as in this example we have two "different" mutations (exon 2 mutation distinct from exon 15 and V600E mutation)-this is for really important for my downstream analysis, as we are searching specific mutations regarding KRAS/BRAF genes-
from previous posts (Only the longest transcript while annotating with Annovar?) I saw that a suggestion would be to choose the longest transcript-however, are there any additional selection criteria to choose one transcript per mutation ?
Thank you in advance,