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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 CNVnator in haploid organisms #251

Open pabloangulo7 opened 2 years ago

pabloangulo7 commented 2 years ago

Hello,

I would like to use this tool to examine the copy number variation in whole genome sequence, germline, haploid organism data. It would be possible? If so, which parameters should I modify?

Thanks

Pablo

abyzov commented 2 years ago

Hi, yes it should be possible. You don’t need to modify any parameters. But you may want to filter calls based on their RD, i.e., normalized RD for deletions must be close to 0, while normalized RD for duplication must be close to 2 or higher.

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