MAPQ mapping quality

Question

[sami]

I would like to filter only mapped reads with hight MAPQ. I use bowtie2 What value should i give to MAPQ? i would like to make variant calling after filtering good reads from bam.

Answer 1

[Ram]

Useful links:

• https://sequencing.qcfail.com/articles/mapq-values-are-really-useful-but-their-implementation-is-a-mess/
• http://biofinysics.blogspot.com/2014/05/how-does-bowtie2-assign-mapq-scores.html