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Old 06-25-2010, 04:15 PM   #2
nilshomer
Nils Homer
 
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Location: Boston, MA, USA

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Quote:
Originally Posted by jlfmssm View Post
I am new for NGS data.
How to check reads are properly paired from SAM file?
It is appreciated someone can point me some programs?

Thanks,
Aimin
Use 'samtools view -X <in.bam>'. All reads with a capital "P" in the flag field are properly paired.
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