Most represented reads in SAM file

Question

[Picasa]

Hi,

I am looking for your help.

I have a SAM file (with paired reads that I have mapped against a reference) and I would like to extract the paired read which is the most represented (or most abundant). I want to select the paired read the most covered for a particular reference.

Is there a tool for this ?

Thanks.

[Pierre Lindenbaum]

what's your criteria for "most represented" ? very same sequence ? match the same overlapping segment ? ...

[Picasa]

Yes same sequences (at 100%).

[GenoMax]

Mapping to the same location for both reads?

Answer would depend largely on what aligner you used and how it treated multi-mappers. ( e.g. with bbmap using the option ambig=all would be needed to get all locations where a read-pair aligns). Aligners may not report all alignments by default.

[Picasa]

Sorry I forgot to mention that I use BWA with the option -M

And yes mapping the same location (because the same reads).