Most represented reads in SAM file
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.
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what's your criteria for "most represented" ? very same sequence ? match the same overlapping segment ? ...
Yes same sequences (at 100%).
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
bbmapusing the optionambig=allwould be needed to get all locations where a read-pair aligns). Aligners may not report all alignments by default.Sorry I forgot to mention that I use BWA with the option -M
And yes mapping the same location (because the same reads).