Mismatch and Indel rate in alignment

Question

[BDK_compbio]

I am using BWA to align the raw reads against a contig set. I would like to know the overall mismatch rate as well as indels in the entire alignment (SAM/BAM). I tried various options of samtools/bamtools, but could not able to find this.

Answer 1

[prasundutta87]

check this out Mismatch and Indel statistics from BAM/SAM file