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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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"Assuming male individual!" output #265

Closed lgmgeo closed 2 years ago

lgmgeo commented 2 years ago

Hi,

During the CNV call step:

$cnvnatorPATH/cnvnator -root sample.root -call 1000 > sample_cnvnator.out

CNVnator (V0.4.1) returns the following message on my male samples:

Assuming male individual!

With female samples, CNVnator returns no message.

Can you explain how CNVnator assumes the gender of the sample (correctly in my samples)?

Many thanks,

Véronique

abyzov commented 2 years ago

Hi, it is based on coverage of autosomes and sex chromosomes.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Associate Professor of Biomedical Informatics, Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, 200 1st street SW, Harwick 3-12 Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978

lgmgeo commented 2 years ago

Ok, thanks. PS: Could be nice to also have "Assuming female individual!" in the output

lgmgeo commented 2 years ago

gender normalization: cf #129