Normalized non-synonymous variant count

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8.8 years ago

qwzhang0601 ▴ 80

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

SNP gene • 2.0k views

ADD COMMENT • link updated 17 months ago by Ram 43k • written 8.8 years ago by qwzhang0601 ▴ 80

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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....

ADD REPLY • link updated 17 months ago by Ram 43k • written 8.8 years ago by karl.stamm 4.1k

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Thanks. Do you prefer to use the length of longest CDS instead of the longest transcript?

ADD REPLY • link updated 17 months ago by Ram 43k • written 8.8 years ago by qwzhang0601 ▴ 80

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