Tool for calculating nucleotide transversion/transition rates

torchij · 02-12-2013, 03:31 PM

Hi all,

Does anyone know of a good tool to calculate SNV transition/transversion profiles??
Meaning the proportion of C>A, T>C C in CpG mutations etc... givin a list of mutations?

The hardest part is getting the CpG contexts. It's relatively easy to code given a list of ref to alt bases, but it's much more complicated for me to annotate the neighbouring base!! I was wondering if there was a good tool for this.

Many thanks,

- Torch

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02-12-2013, 03:31 PM	#1
torchij Junior Member Location: Toronto Join Date: Jul 2012 Posts: 1	Tool for calculating nucleotide transversion/transition rates Hi all, Does anyone know of a good tool to calculate SNV transition/transversion profiles?? Meaning the proportion of C>A, T>C C in CpG mutations etc... givin a list of mutations? The hardest part is getting the CpG contexts. It's relatively easy to code given a list of ref to alt bases, but it's much more complicated for me to annotate the neighbouring base!! I was wondering if there was a good tool for this. Many thanks, - Torch