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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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multiancestry-PFB #68

Open psychrb opened 3 years ago

psychrb commented 3 years ago

What's the general guidance for generating PFB files for a multi ancestry cohort that is genotyped? How should generation of PFB files (or PennCNV) be approached alternatively for a multi-ancestry cohort..compared to a cohort of uniform ancestry..Thanks.

kaichop commented 3 years ago

In practice the actual PFB values have minor influence on CNV calling. So it is totally fine to use multi-ancestry cohort to build PFB files, which actually increase the likelihood of polymorphic alleles. This allows more unbiased comparison of CNV calls on multiple cohorts, when using the same PFB file for CNV calling.

On Sun, Feb 14, 2021 at 6:01 AM psychrb notifications@github.com wrote:

What's the general guidance for generating PFB files for a multi ancestry cohort that is genotyped? How should generation of PFB files (or PennCNV) be approached alternatively for a multi-ancestry cohort..compared to a cohort of uniform ancestry..Thanks.

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