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Old 05-13-2011, 09:19 AM   #1
Location: canada

Join Date: Sep 2009
Posts: 29
Default CNV analysis on Illumina / Solid genomes

Hi all,

I had a look at the wiki and I see there are many tools available for getting copy number changes from read alignments. I am wondering if there is a particular accepted tool that comes most highly recommended.

I am most often comparing 30X tumour to 30X normal, and I know from experience that GC bias correction is necessary.

Freec seems like a good candidate however, when comparing matched tumour normal pairs the applied bias correction seems a little less vigorous than I would like.

Any information is appreciated!
rcorbett is offline   Reply With Quote
Old 07-05-2012, 04:36 AM   #2
Location: Paris

Join Date: Sep 2008
Posts: 69

I think when you have 30X coverage, FREEC must be a good choice. In addition to copy numbers it will detect LOH regions and it could tell you which regions of gain/loss/LOH are likely to be somatic/germline.
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Old 07-05-2012, 11:04 AM   #3
Location: Texas

Join Date: May 2010
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Default XHMM for CNV analysis


Has anyone tried the xhmm CNV tool on exomes?

I tried it on five exome bams and I always get an empty vcf file!

unagaswamy is offline   Reply With Quote
Old 07-06-2012, 07:27 AM   #4
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Location: Indiana University, Indiana, USA

Join Date: Jul 2012
Posts: 8

I haven't used this software myself, but I have been looking into CNV software as well, and saw this. While it isn't what I'm looking for, it seems like it could be very useful to you since you are using tumor/normal comparison data.

The software is VarScan (, and a specific section of the software is for finding CNV between normal/abnormal(tumor) samples. Here is the section on that:

CraigJ is offline   Reply With Quote

cnv, copy number, read alignment

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