Get identical mapped nucleotide length from bowtie2 generated SAM files

Question

[hdy]

I used bowtie2 to map my reads to a reference genome and get the SAM files returned. I am wondering if there is a way to get the length of the identical mapped nucleotide length. Basically I want to get a hamming distance or identical mapping vs total read length ratio from the SAM files.

Answer 1

[hdy]

find out the answer in another post: How To Find Out The Mismatchs Of An Alignment Entry In The Sam File?