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menenuh 01-28-2010 05:17 AM

Alignment statistics from bwa?
Hello, I am a newbie and I have a question,
Is it possible to get alignment statistics from sam output of bwa algorithm? And also, what happens to unaligned reads? Are there also present in the generated sam file? I have several 0's in the FLAG field in the sam output, is it an unmapped read?
Well, it seems like I have more than one question :)

lh3 01-29-2010 01:14 PM

You may get SAM output and then convert it to BAM. samtools flagstat will give you a brief stats. Unmapped reads are stored in the SAM file.

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