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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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extract depth information from .root file #161

Closed seoldh closed 3 years ago

seoldh commented 5 years ago

Hello I am a beginner in bioinformatics.

While studying CNV, I want to calculate Vst value from my data.

It seems to be using the variance of depth,

but how can I extract depth information from the specific region that is not CNV region?

Or is there any other easy way to calculate it?

Also, when I use '-view' command, I get the following error

cnvnator -root output.root -view 300

1:100-1000 Error in : out of bounds: i = -1, Length = 0

How can I fix it?

Thank you.

abyzov commented 5 years ago

Hi, do you specifically need coverage or genotype is good enough? There is currently no function to return coverage for a given region. You can use -genotype functionality to estimate copy number. You can also consider using -eval functionality to estimate average RD and its variance.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant 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