Mate Pair Alignment Summary

Question

[Richard]

Hi all, I have vague memories of running an aligner on mate-pair data and having it generate a summary of how many read pairs made proper mate-pairs, paired ends, or unexpected orientations.

Can anyone tell me if they know of an aligner that does this?

[Rm]

run samtools flagstat on the alignment bam file

[Sean Davis]

Consider converting this from a comment to an answer so that others can see that the question has been answered?

Answer 1

[Rm]

run samtools flagstat on the alignment bam file