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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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How are you determining Genotype #274

Open anman1227 opened 1 year ago

anman1227 commented 1 year ago

Hello. I was wondering if you couple explain how you are determine the genotype for a cnv. Specifically for each allele what criteria are you using to label it as a 1 or a 0. Thank you very much

abyzov commented 1 year ago

Hi, in the output of calling normalized RD is the value relative to the average RD. When using -genotype function the result is normalized rd scaled by 2 for diploid chromosome and scaled by 1 for haploid 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

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anman1227 commented 1 year ago

I see. Thank you very much for the quick response. I was also wondering when you determine that you are unable to make a call regarding the genotype (for instance label a genotype as "./1"). Thank you very much

abyzov commented 1 year ago

Not sure what you mean. Probably ./1 refers to haploid 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