[Biopython] coverage calculating from BAM

[Peter Cock]

On Thu, Mar 1, 2012 at 7:50 AM, Mic <mictadlo at gmail.com> wrote:
> Hello,
> How is it possible to calculate coverage from a BAM file in format eg.
> 10x coverage?
>
> Thank you in advance.

Normally we'd talk about coverage as it varies along the genome,
perhaps using a sliding window. This is often represented using
a wiggle file or a BigWig file - and there are scripts for computing
these from SAM/BAM alignments.

Are you looking for a single number the entire BAM file?

Peter

P.S. What does this have to do with pysam or Biopython?