Frequency of A, C, T, or G at every position in SAM file

[M4TTN]

Dear all,

We would like to extract the read depth of each base type (A, C, T or G) for every position of our aligned reads (a SAM file created using Bowtie2).

Does anyone know of a tool that does this?

The closest link I found here was:

http://seqanswers.com/forums/showthread.php?t=38630

But I'm not sure that would be appropriate for use with aligned genome data.

Many thanks

[dariober]

Hi- I think pysamstats can do what you need.

[M4TTN]

Dear dariober,

We've got pysamstats up and running and it seems to be generating exactly the kind of output we require!

Many thanks for your help, Matt