Extract perfectly mapped reads from SAM/BAM file

[Graham Etherington]

Hi,
Given a SAM or BAM file, does anyone know how to identify which paired-sequences map perfectly to the reference? By perfectly mapped, I mean that the query is identical to the the reference (or its reverse complement).
I'm fine using either command-line tools or programming.
Many thanks,
Graham

[dariober]

Hi,
I think you can look at the NM tag in the SAM/BAM file. If both reads of a pair have NM:i:0 than the match is perfect.

Dario

[nilshomer]

Make sure that there is also no soft-clipping in the cigar if you want the full read aligned.