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Old 02-27-2013, 07:47 AM   #1
Junior Member
Location: Southampton

Join Date: Feb 2013
Posts: 4
Angry Problems running ExomeCNV

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.


lkadalayil is offline   Reply With Quote
Old 04-02-2013, 04:08 PM   #2
Location: San Francisco, CA

Join Date: Aug 2011
Posts: 91

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:
... unfortunately that doesn't tell me too much how to get it started.
lethalfang is offline   Reply With Quote
Old 07-23-2013, 01:06 AM   #3
Senior Member
Location: Hong Kong

Join Date: Mar 2010
Posts: 497

I don't use

read.coverage.gatk works for me
ymc is offline   Reply With Quote

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