setting control genome ploidy

BoevaLab / FREEC

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data

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setting control genome ploidy #63

Open Aborneman opened 5 years ago

Aborneman commented 5 years ago

Hi, I am working on using FREEC to call CNVs in a triploid organism and was wondering if the "ploidy" variable refers to both the expected ploidy of the control and sample or just the sample (it appears to use ploidy=2 for the control no matter what is set here)? Thanks, Anthony

valeu commented 5 years ago

PLoidy of the control is assumed to be 2. Do not use the control (but GC correction) if the control ploidy is also 3.