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Old 08-29-2012, 01:13 PM   #2
jujubix
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Location: Vancouver

Join Date: May 2011
Posts: 14
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I briefly did some work determining CNV events in matched tumour/normal pairs, from my experience, the difference in coverage between libraries can be corrected for by normalizing the read counts.

Some tools for determining CNV and LoH that worked for me include:

HMMcopy for normalizing, identifying and classifying CNV events in matched and/or unmatched tumour samples:
http://compbio.bccrc.ca/software/hmmcopy/

Apolloh, the accompanying software used to determine LoH events:
http://compbio.bccrc.ca/software/apolloh/

Both were used to determing CNV and LOH events in a recent study here:
http://www.nature.com/nature/journal...ture10933.html
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