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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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Parameter -d in Generate histogram affect the CNV calling #221

Closed YYDbi closed 3 years ago

YYDbi commented 4 years ago

Hello,

  When I use the CNVnator_v0.3 to do the CNV calling, I find the parameter -d in Generate histogram shows a large effect in the last CNV calling result. The number of CNV will be twice larger than without -d parameter. We had both provide the -genome and -d (with all chromosome sequence in the directory). I find the number of CNV results without -d is more than with -d, and also is longer than when they had the same CNV, Did the -d sequence provide the filter or check function?
  Additionally, I had check the problem with CNVnator-0.3.2_yepp, this one will generate a similar results both with -d or without -d, and it also similar to CNVnator_v0.3 with -d in  Generate histogram.

Thanks for any advice.

abyzov commented 4 years ago

Hi, please check the output to see whether there was GC correction done with and without -d option.

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