How to find out longest transcript from Annovar annotation output

Question

[sunilpachakar]

I have annovar annotation data, In this data Amino acid change column shows multiple transcripts with multiple mutations and I want to take only one single mutation for my further analysis. As per Annovar documentation use of the longest transcript in this situation will be beneficial. Is there any way to find the longest transcript from Annovar data output? Following is my Annovar output file.

chr1    45797153    45797153    A   T   exonic  MUTYH   .   nonsynonymous SNV   MUTYH:NM_001350650:exon12:c.T833A:p.L278Q,MUTYH:NM_001350651:exon12:c.T833A:p.L278Q,MUTYH:NM_001048171:exon13:c.T1220A:p.L407Q,MUTYH:NM_001048172:exon13:c.T1181A:p.L394Q,MUTYH:NM_001048173:exon13:c.T1178A:p.L393Q,MUTYH:NM_001048174:exon13:c.T1178A:p.L393Q,MUTYH:NM_001128425:exon13:c.T1262A:p.L421Q,MUTYH:NM_001293190:exon13:c.T1223A:p.L408Q,MUTYH:NM_001293191:exon13:c.T1211A:p.L404Q,MUTYH:NM_001293192:exon13:c.T902A:p.L301Q,MUTYH:NM_001293196:exon13:c.T902A:p.L301Q,MUTYH:NM_012222:exon13:c.T1253A:p.L418Q,MUTYH:NM_001293195:exon14:c.T1178A:p.L393Q

Answer 1

[Ram]

I wonder why this post has a software error tag - ANNOVAR seems to be working as it is supposed to.

In any case, you'll need to re-run ANNOVAR with a canonicall transcript option (if available) or split ANNOVAR output into one effect per line and then filter based on a dataset that maps each HUGO symbol to its longest/canonical transcript. To create this dataset, search the website for posts that get the longest transcript across the genome - the solution will involve wrangling output from UCSC genome browser's MySQL database (and will in all probability be from Pierre Lindenbaum )