When I try to process my exome data bam files using DepthOfCoverage under GATK tools (on the main instance),  the program seems to keep running forever without ever completing.  There is no error message output but the program never ends after going for several days! Could it be something wrong with my files or has any one else reported having an issue with it?

Regards,

Tom 

---------------------------------------------

Thomas Jaworek

Department of Ophthalmology

Cincinnati Children's Hospital

3333 Burnet Avenue

Research Building R2409 

Cincinnati, OH 45229

thomas.jaworek@cchmc.org

513-803-2951