samtools mpileup: position of each base within their reads

Question

[abascalfederico]

I'm using samtools mpileup to analyse which bases align to each genomic site. In addition to base qualities (which are easily accessible from mpileup's output) I would like to know the position of each of the bases within their corresponding reads. I want to analyse the patterns of variation at beginning and end of reads. I know mpileup tells you when a base comes from the beginning or the end of a read, but I would like something more precise, the exact position within a read for each base.

Can I do this with samtools-mpileup? Is there any other software to help me do this analysis?

Thanks!

Federico

[Devon Ryan]

You'd need to use the API for this. The pysam module in python might be the simplest route.

[abascalfederico]

Thank you! I found pysam very easy to use - a new door opens to more complicated but powerful analyses