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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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Read depth not normalized to 1? #159

Closed osowiecki closed 3 years ago

osowiecki commented 5 years ago

Shouldn't RD_value come between 0 and 1 after dividing the genotype value by 2? I used bin size of 200 in this example. The 10:3799001-3800000 region has one large positive RD outlier.

10:3799001-3800000 genotype Genotype 10:3799001-3800000 /data/CF_6916.root 2235.65 2201.77 10:20001-25000 genotype Genotype 10:20001-25000 /data/CF_6916.root 4.76189 4.68972 10:449195-450225 genotype Genotype 10:449195-450225 /data/CF_6916.root 0.779528 0.767713

I was tracking the source code this night and I still don't know how it got to 2201.77. I'm trying to use CNVnator genotyping tool and cnvnator2VCF.pl code to give some kind of GT field to the "ERDS" result vcf file.

[EDIT] :

I can see in :

https://github.com/abyzovlab/CNVnator/issues/153

That I can treat genotype RD value as estimated CNV number. This makes sense and gives similar copy number counts to ERDS. This pretty much solves my problem, yet I would still like to know if normalized RD value calculation behaves normally when generating such large values above 1.

abyzov commented 5 years ago

Hi, genotype can be of any value. You can use -view functionality to check RD in the region of interest.

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