Extract improperly paired read from BAM file

Question

[godth13teen]

Hi, I want to do manual checking on my BAM file after getting the statistic from samtools flagstat. I tried to extract the improperly paired read but failed to do so far.

I tried to use awk to extract read not contain 2 flagstat, but it's not working because the flagstat is bitwise and combined.

Thank you for your advice.

Answer 1

[swbarnes2]

Don't use awk. Use samtools view.