CNV in Normal Samples?
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twtoal • 0
@twtoal-15473
Last seen 8 days ago
United States

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

 

PureCN Germline Normal CNV • 402 views
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@markusriester-9875
Last seen 10 days ago
United States

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).

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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?).

 

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