Question: How to calculate the mapping rate from BAM files generated from BWA
0
gravatar for wangdp123
4 weeks ago by
wangdp123140
Oxford
wangdp123140 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
ADD COMMENTlink written 4 weeks ago by wangdp123140
2
gravatar for h.mon
4 weeks ago by
h.mon24k
Brazil
h.mon24k wrote:

samtools flagstat. See also samtools stats and samtools idxstats.

ADD COMMENTlink modified 29 days ago • written 4 weeks ago by h.mon24k
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