Problems running ExomeCNV

lkadalayil

Junior Member

Join Date: Feb 2013

Posts: 4
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#1

Problems running ExomeCNV

02-27-2013, 07:47 AM

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
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lethalfang

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Join Date: Aug 2011

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#2

04-02-2013, 03:08 PM

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.
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ymc

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Join Date: Mar 2010

Posts: 496
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#3

07-23-2013, 12:06 AM

I don't use bam2coverage.sh

read.coverage.gatk works for me
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