Normalized non-synonymous variant count
I am analyzing 1000 genome data and get the annotation of SNP by ANNOVAR. Now I want to normalize the synonymous and non-synonymous variant count in a group of genes according to the length of genes. Because each gene may have different isoforms, I choose the longest transcripts and use their lengths. I wonder whether it is right? should I use the length of CDS (since there are UTR in transcript, which are not translated)? Thanks
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Well you're probably not going to have any non-synonymous mutations in an untranslated region. So If you want the numbers to skew....
Thanks. Do you prefer to use the length of longest CDS instead of the longest transcript?