How are you determining Genotype

[anman1227]

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]

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.org<http://www.abyzovlab.org> tel: +1-(507)-538-0978 Message ID: ***@***.***>

[anman1227]

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]

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.org<http://www.abyzovlab.org> tel: +1-(507)-538-0978