Any tool to review the maps statistics?

[arkilis]

Hi all,

Anyone can sugguest one tool to give out statistics on the sam/bam files?
I tried the samtools flagstat to do this, but it only generate very limited information here.

It will be great to know which sequence has been aligned to which read.

Thanks,
Ben

[GenoMax]

See #4 and 5 posts: http://seqanswers.com/forums/showthread.php?t=49935

[arkilis]

See #4 and 5 posts: http://seqanswers.com/forums/showthread.php?t=49935

Qualimap gives out detailed mapping info but failed to generate things like which read has been mapped to which sequence.

Thanks a lot!