Problems running ExomeCNV

[lkadalayil]

I want to run ExomeCNV on some of my bam files. I tried to use bam2coverage to convert the bam files to coverage files with no success. I used the version of samtool specified in the User Guidebook. Yet the output contains zeros in the last 4 coloumns. Any ideas how to get around this?

I noticed that there is a post from Emily who had the same problem. However none have posted an answer. It would so helpful for me to know how Emily solved this problem.

Thanks

Latha

[lethalfang]

I've just run across that program and want to give it a try.
Are you aware of a user-friend user's manual or tutorial somewhere?
I have the PDF file in CRAN: http://cran.r-project.org/web/packag...V/ExomeCNV.pdf
... unfortunately that doesn't tell me too much how to get it started.

[ymc]

I don't use bam2coverage.sh

read.coverage.gatk works for me