I've added our BAM-QC/Coverage tool to the toolshed. Search for 'coverage_report'

http://toolshed.g2.bx.psu.edu/repository/view_repository?sort=name&operation=view_or_manage_repository&id=5616f9aed501df32

It generates a pdf plot similar to the attached one (full exome set, but only a few genes in bed file for demo purposes).

Best,

Geert

On 09/04/2013 09:59 PM, shamsher jagat wrote:

I am looking for a tool to perform QC of Bam file especially following functions:
1. BAsic information and stat.

2. Coverage across reference features- gene/ transcripts.

Is it possible to do it in Galaxy?

Thanks

-- 

Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandeweyer@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/pub/geert-vandeweyer/26/457/726