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Old 08-24-2012, 10:48 AM   #1
shyam_la
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Location: California

Join Date: Mar 2012
Posts: 97
Default Need help with CNV..

Hi,

I'm relatively new to bioinformatics. Have mastered SNVs and indels for the most part.. Now want to try my hand with CNVs.. I'm working with tumor-normal exome data..

My question is, is it still possible to do CNV when my tumor and normal samples are sequenced to varying depths. Lets say the coverage on my tumor data is 90+ on average and on normal reads is 45+ on average. Is CNV still possible to be done? If so which tool should be used and what parameter should be altered?

The analysis need not necessarily be paired. I just want to know which tumor samples have amplifications/deletions and in which regions/genes. I'm also interested in LoH in the tumor sample.

Any help would be appreciated..
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