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5 hours ago by

Greece

Dear Biostars,

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:

BRAF:ENST00000479537.1:exon2:c.T83A:p.V28E,BRAF:ENST00000288602.6:exon15:c.T1799A:p.V600E,

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,

Efstathios



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