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Question: How to calculate the mapping rate from BAM files generated from BWA
0
gravatar for wangdp123
8 months ago by
wangdp123 • 190
Oxford
wangdp123 • 190 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 • 441 views
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written 8 months ago by wangdp123 • 190
2
gravatar for h.mon
8 months ago by
h.mon ♦ 28k
Brazil
h.mon ♦ 28k wrote:

samtools flagstat. See also samtools stats and samtools idxstats.
ADD COMMENT • link modified 8 months ago • written 8 months ago by h.mon ♦ 28k
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