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Question: How to calculate the mapping rate from BAM files generated from BWA
0
gravatar for wangdp123
4 weeks ago by
wangdp123 • 140
Oxford
wangdp123 • 140 wrote:

Hi there,

I used BWA MEM to map the paired-end reads onto a genome but it sees that BWA didn't report the mapping metrics such as mapping rate, unique mapping rate, concordant mapping rate, unmapping rate et al.

Is there any way to get this kind of information?

Many thanks,

Tom
bwa • 132 views
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written 4 weeks ago by wangdp123 • 140
2
gravatar for h.mon
4 weeks ago by
h.mon ♦ 24k
Brazil
h.mon ♦ 24k wrote:

samtools flagstat. See also samtools stats and samtools idxstats.
ADD COMMENT • link modified 29 days ago • written 4 weeks ago by h.mon ♦ 24k
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