search

abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
Other
207 stars 65 forks source link

Number of copies for deletion events #213

Closed chirrie closed 3 years ago

chirrie commented 4 years ago

Dear Prof. Abyzov,

Please clarify to me how to interpret the absolute number of copies in case of deletion events.

Take a case where I am using cutoff <0.4 for deletion events.

So does it mean any CNV loci with normalized read depth being 0.4 have zero absolute copy numbers?

From my previous question to you, you mentioned that if read depth is 0.11 the number of copies will be approximately zero.

So what of cases where normalized read depth is 0.34 for instance? or 0.25?

In case of duplication, I hope I am right to say that absolute copies are 2 if read depth is 1.76( rounded to nearest integer)

abyzov commented 4 years ago

It is up to you but I would think that it is logical to assume that:

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

On Jul 21, 2020, at 12:23 PM, Vivien Chebii notifications@github.com<mailto:notifications@github.com> wrote:

Dear Prof. Abyzov,

Please clarify to me how to interpret the absolute number of copies in case of deletion events.

Take a case where I am using cutoff <0.4 for deletion events.

So does it mean any CNV loci with normalized read depth being 0.4 have zero absolute copy numbers?

From my previous question to you, you mentioned that if read depth is 0.11 the number of copies will be approximately zero.

So what of cases where normalized read depth is 0.34 for instance? or 0.25?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/abyzovlab/CNVnator/issues/213, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACLKGOIEXZMJBYDLJX23BATR4XFKBANCNFSM4PD2HGVA.

chirrie commented 4 years ago

Thank you for the feedback

Will be right to say the number of copies is zero if normalized read depth is <0.5 for deletion

From what CNVnator reports as normalized RD say 0.25 for deletion or 5.6 for duplication does it represent haploid or diploid?

abyzov commented 4 years ago

Sorry, it could be confusing. In the output of -call RD is normalized to 1, i.e., RD for non-CNV region is 1. In the genotyping step RD is normalized to 2 for chr1-22 and 1 for chrX,Y.

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