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Question: CNV in Normal Samples?
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gravatar for twtoal
10 weeks ago by
twtoal0
twtoal0 wrote:

Can PureCN be used to call CNVs in normal germline samples, using the pool of normals database to provide a standard normal reference?

 

ADD COMMENTlink modified 10 weeks ago by markus.riester110 • written 10 weeks ago by twtoal0
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gravatar for markus.riester
10 weeks ago by
markus.riester110 wrote:

I would use specialized tools for germline. We use a very similar coverage normalization as GATK4 and this comes with a germline workflow. But there are many others. 

If you really want to use PureCN, make sure that the normal is not in the pool and do not provide a target weights file (for somatic calling, we try to ignore exons that have a high variance in the PoN). You can try the recommended settings for cell lines (Quick vignette).

ADD COMMENTlink written 10 weeks ago by markus.riester110

Ok.  It would be very nice to be able to use PureCN for the germline too, for consistency's sake if nothing else.  Leaving the normal out of the pool would require making a separate pool file for each normal.  It would be nice if there were a way to tell PureCN to ignore a particular sample in the pool (or is the pool already a blend of all its input samples?).

 

ADD REPLYlink written 10 weeks ago by twtoal0
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