How to calculate the mapping rate from BAM files generated from BWA

Question

[wangdp123]

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

Answer 1

[h.mon]

samtools flagstat. See also samtools stats and samtools idxstats.