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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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Running CNVnator using scaffolds #223

Closed chirrie closed 3 years ago

chirrie commented 4 years ago

Dear Prof Abyzov,

I intend to use a genome that has scaffolds in place of chromosomes as reference for copy number variation detection using CNVnator. I have read the CNVnator manual at it seems it only accepts chromosomes. I am wondering if there is a way to tailor it to work with scaffolds.

abyzov commented 4 years ago

Hello, CNVnator parses genome information from bam header. So, you should be able to work with scaffolds.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Associate Professor of Biomedical Informatics, Department of Health Sciences Research, 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 fax: +1-(507)-284-0745