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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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Bin size for 20x depth of coverage #275

Closed zainabae closed 1 year ago

zainabae commented 1 year ago

Hello, I’m little bit confused about selecting the appropriate bin size. Actually I am not looking for specific CNV region, I want to get as much as possible CNV regions among my samples.

I’m working on CamDro3 reference genome, My samples have approximately 20x depth of coverage and the reads lengths 15-150.

The table here does not include bin size for 20X.

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And I found this page explaining the paper with different values other than those mentioned in the table (it is mentioned that with 20 and 30x the 100 bin size is appropriate)

However bin size of 100 is shorter than some of my reads lengths since I have reads (15-150)

http://avrilomics.blogspot.com/2013/01/using-cnvnator-to-find-copy-number.html?m=1

image

So anyone can help me in selecting the appropriate bin size for my samples?

abyzov commented 1 year ago

Hi, choice of bin size also depends on the variance in the data. For you coverage and read length I’d suggest to start from 500 bp bins

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

zainabae commented 1 year ago

@abyzov thank you 👍🏻