Question: How to calculate the mapping rate from BAM files generated from BWA
0
gravatar for wangdp123
8 months ago by
wangdp123190
Oxford
wangdp123190 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
ADD COMMENTlink written 8 months ago by wangdp123190
2
gravatar for h.mon
8 months ago by
h.mon28k
Brazil
h.mon28k wrote:

samtools flagstat. See also samtools stats and samtools idxstats.

ADD COMMENTlink modified 8 months ago • written 8 months ago by h.mon28k
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