Extract perfectly mapped reads from SAM/BAM file

Graham Etherington · 07-20-2011, 05:45 AM

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 · 07-20-2011, 08:44 AM

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 · 07-21-2011, 08:27 AM

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

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07-20-2011, 05:45 AM	#1
Graham Etherington Member Location: Norwich, England. Join Date: Apr 2010 Posts: 22	Extract perfectly mapped reads from SAM/BAM file 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

07-20-2011, 08:44 AM	#2
dariober Senior Member Location: Cambridge, UK Join Date: May 2010 Posts: 311	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

07-21-2011, 08:27 AM	#3
nilshomer Nils Homer Location: Boston, MA, USA Join Date: Nov 2008 Posts: 1,285	Make sure that there is also no soft-clipping in the cigar if you want the full read aligned.