Whole Exome CNV tools

Question

[BAGeno]

Hi,

I want to ask that can we use breakerdancer, manta,delly, lumpy-sv for copy number variation calling of whole exome analysis? I have just whole exome data of five patients and I want to call their copy number variations.

[gregorymcinnes]

Did you find a good tool to use? I have the same problem.

Answer 1

[ReWeeda]

Hi BAGeno!

There are plenty of tools out there for CNVs detection from WES data! In addition to VarScan, cited by 2nelly, you can also try with:

• Sequenza
• XCAVATOR
• ADTEX
• iCNV
• CONTRA
• FREEC
• CNVkit

I also suggest you to read this article.

I worked on CNVs detection in the recent past, and I developed a simple wrapper for a CNV simulator developed by NabaviLab that I found a little bit complicated in the first place. (WARNING : Simulation is slow!)

You can maybe simulate reads similar to you real data (similar depth of coverage, similar balancing in term of amplifications and deletions given what you expect to find, etc) with CNVs inserted in known place and then test the different tools to find which one suits better your task!

Hope this helps!

[tanbiswas6]

Hi ReWeeda,

I've used FREEC and CNVkit to analyze CNV profile fro WES tumor samples. In both cases the output profile looked noisy. Please see these links: 1) CNVkit problem: C: CNVKit noisy scatter plot 2) FREEC: CNV Profile figure

Please suggest something. Can I use CNVbencher for WES data? Thanks!

Answer 2

[2nelly]

Hi BAGeno,

I would suggest you to use VarScan, which is designed specifically for the type of data you have (WES).

Somatic Copy Number Alteration (CNA) Calling

Cheers!

[BAGeno]

Thanks for your suggestion but VarScan is for tumor normal pair exome data. My patients are not cancer patients.