Abnormal Average RD and results when use cnvnator

[Chipmunks22]

Hi ! I'm using cnvnator to call CNV with my WES data.This is the command I use:

cnvnator -root sample.root -tree sample.bam -chrom $(seq 1 22) X Y -genome hg19
cnvnator -root sample.root -his 1000 -chrom $(seq 1 22) X Y -d /path_to_chr.fa
cnvnator -root sample.root -stat 1000 -d /path_to_chr.fa
cnvnator -root sample.root -partition 1000
cnvnator -root sample.root -call 1000  >sample.txt

When I use cnvnator -root sample.root -partition 1000 -d /path_to_chr.fa, I get this message：
Average RD per bin (1-22) is 0.245291 +- 2.51832 (before GC correction)
Average RD per bin (X,Y) is 7.09492e-14 +- 2.14621 (before GC correction)
Correcting counts by GC-content for '1' ...
Zero value of GC average.
Bin 13103 with center 1.31025e+07 is not corrected.
Correcting counts by GC-content for '2' ...
Correcting counts by GC-content for '3' ...
Zero value of GC average.
Bin 145439 with center 1.45438e+08 is not corrected.
Correcting counts by GC-content for '4' ...
Correcting counts by GC-content for '5' ...

The "Average RD per bin"looks abnormal,dose it too samll?
Despite this,I find that the normalized_RD in my results is abnormal too.It haven't been normalized that the value is larger than 1. Why dose this happen?

[abyzov]

Hi, sorry for later reply. CNVnator is not designed to be used with WES data. You can try to do so at your own risk. If you do then you have to use large bins size to make sure that most bins get good amount of mapped reads. As I see from the output you provided coverage per bin you are using (1000 bp) is too small. 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 7-91 Rochester, MN 55905 www.abyzovlab.org tel: +1-(507)-538-0978 On Mar 21, 2023, at 12:19 PM, Chipmunks22 ***@***.***> wrote: Hi ! I'm using cnvnator to call CNV with my WES data.This is the command I use: cnvnator -root sample.root -tree sample.bam -chrom $(seq 1 22) X Y -genome hg19 cnvnator -root sample.root -his 1000 -chrom $(seq 1 22) X Y -d /path_to_chr.fa cnvnator -root sample.root -stat 1000 -d /path_to_chr.fa cnvnator -root sample.root -partition 1000 cnvnator -root sample.root -call 1000 >sample.txt When I use cnvnator -root sample.root -partition 1000 -d /path_to_chr.fa, I get this message： Average RD per bin (1-22) is 0.245291 +- 2.51832 (before GC correction) Average RD per bin (X,Y) is 7.09492e-14 +- 2.14621 (before GC correction) Correcting counts by GC-content for '1' ... Zero value of GC average. Bin 13103 with center 1.31025e+07 is not corrected. Correcting counts by GC-content for '2' ... Correcting counts by GC-content for '3' ... Zero value of GC average. Bin 145439 with center 1.45438e+08 is not corrected. Correcting counts by GC-content for '4' ... Correcting counts by GC-content for '5' ... The "Average RD per bin"looks abnormal,dose it too samll? Despite this,I find that the normalized_RD in my results is abnormal too.It haven't been normalized that the value is larger than 1. Why dose this happen? — Reply to this email directly, view it on GitHub<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fabyzovlab%2FCNVnator%2Fissues%2F277&data=05%7C01%7CAbyzov.Alexej%40mayo.edu%7Cb3d0fa637a564a90a2fc08db29ed6ea2%7Ca25fff9c3f634fb29a8ad9bdd0321f9a%7C0%7C0%7C638149871979883051%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=GBwHWbDRYxG%2Brhu8FT%2FDLEnbMFLu1MmxgHfnz6OcXNQ%3D&reserved=0>, or unsubscribe<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FACLKGONB6ETXXNDJFQUNB43W5FXDNANCNFSM6AAAAAAWCE5BGE&data=05%7C01%7CAbyzov.Alexej%40mayo.edu%7Cb3d0fa637a564a90a2fc08db29ed6ea2%7Ca25fff9c3f634fb29a8ad9bdd0321f9a%7C0%7C0%7C638149871979883051%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Cmky5d77Zm%2FdtU4D9PXRHiLhK0mbfOTvARLQV%2BYQ7LI%3D&reserved=0>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>