What are currently the best copy number variantion calling tools?
Is there a distinction between the best tools suited for whole genome or exome data? Or are the tools that claim to be good at CNV calling for exome data (for instance Varscan) also well suited for CNV calling in whole genome data?
Are there more of these distinctions between CNV caller tools?
Hi, I have very good experiences with CNVkit - this is very robust tool and works perfectly fine for Capture enrichment library (also author mention good results for WGS and Amplicon panels, but did not validate). We are right now validating this tool and looks perfectly fine. This tool is very fast a and lot of usable statistics and graphs are generated. Really good job and hats off to author!
Look at this page.
This answer may shed a little light on the difference between exome and whole genome copy number calling: Bias During Exome Capture For Cnv Analysis
In short, no - the algorithms have significant differences and cannot be used interchangeably.
A quick search here on Biostar will turn up the names of lots of tools you can try - I haven't benchmarked many of the more recent ones.
Call me biased, but take look at the cn.mops package (Bioconductor). The algorithm was published in Nucleic Acids Research and the paper can be found here
CNVnator from the Gernstein lab at Yale is a CNV calling tool that is mentioned often in SV / CNV (review) papers.
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version 2.3.6
Next to exome - whole genome another important difference between the tools is that some require matched case-control samples (like CNV-seq) and some do not (like ControlFreec). While you are waiting for a better answer/comment this list of CNV tools for NGS sequencing might be worth looking at.
Apparently, ControlFreec DOES handle the matched case-control. From the second paragraph of the link you provided : "The control (matched normal) sample is optional."
Sorry, meant require, changed it
Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives
There is a huge difference between germline CNVs and somatic CNAs calling.