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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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Use of the "-genome" option? #266

Closed lgmgeo closed 2 years ago

lgmgeo commented 2 years ago

Hi,

I wonder what is the use of the "-genome" option in CNVnator: image

Does CNVnator use this information in its code? Or is it just carried over to the output files?

Many thanks in advance,

Véronique

abyzov commented 2 years ago

Hi, with bam files containing header this option is not necessary. It is only needed for sam files without header.

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

Got it.

Thanks!!