View Single Post
Old 09-06-2012, 06:57 AM   #3
shyam_la
Member
 
Location: California

Join Date: Mar 2012
Posts: 97
Default

Thank you. They seem to be fairly complicated to use.. Will give them a shot..

Quote:
Originally Posted by jujubix View Post
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
shyam_la is offline   Reply With Quote