Question: Calculating Mutation Rate Using Mpileup Files
0
gravatar for QVINTVS_FABIVS_MAXIMVS
6.8 years ago by
USA SoCal
QVINTVS_FABIVS_MAXIMVS2.4k wrote:

Hi all,

I want to calculate the mutation rate for a codon using the mpileup files I generated from paired end reads.

I have 60 samples all mapped to the same reference. So how do I calculate a mutation rate for a codon using the read quality and coverage data? Is there a program that already does this, or is there an algorithm for which I can use for my own script?

I have predicted sites of positive selection, I would like to see if the sequencing reads reflect this prediction.

Thanks!

mutation samtools mpileup pileup • 2.1k views
ADD COMMENTlink written 6.8 years ago by QVINTVS_FABIVS_MAXIMVS2.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1834 users visited in the last hour