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Old 07-27-2011, 10:14 PM   #16
gprakhar
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Location: India

Join Date: Aug 2010
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Quote:
Originally Posted by cdinz View Post
I have the same question too. It would be really great if someone can shed some light on it.
The input type will not vary, it will still be a BAM file aligned to the ref genome.
The difference comes in the analysis part.
You will have to take into consideration the Intron-Exon Junctions. As a Intron will be taken as a CNV. Also another problem is that if a CNV breakpiomt lies in the Intron, you can not come to know about it.
We have tumor Exome data, done by the True-Seq protocol, hence while doing the analysis use the co-ordinates provided by them.
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