[NGSfan]

I found another program for Exome copy number variants called "exomeCopy"

It is part of BioConductor - I have not tried it yet but it looks interesting.

http://www.bioconductor.org/packages/release/bioc/html/exomeCopy.html

[wanguan2000]

Which software is better now, I just have very good data(whole genomes, and exome sequecing) sets can be used to test.

[milesgr]

I know this thread is a bit old, but I tried using ExomeCNV as well and also get 0 in the average coverage column. Did anyone figure out why this occurs? Thanks!

[ymc]

I know this thread is a bit old, but I tried using ExomeCNV as well and also get 0 in the average coverage column. Did anyone figure out why this occurs? Thanks!

Do you have samtools newer than 0.1.16?

If all else fail, you can use GATK to generate coverage file.

[BLC]

we are working on some things at BioDiscovery (http://www.biodiscovery.com) - we make the Nexus Copy Number software. So far, and I think this reflects the consensus -- straight coverage doesn't work in most cases, maybe excepting whole genome, due to a host of systematic biases. There are some decent algorithms for germline samples (xHMM, CoNIFER), but the correction method (SVD) doesn't apply for cancer since it is much more difficult to distinguish artifacts from actual events. There are some other algorithms we've been experimenting with and would love to hear feedback or other ideas.

[Alberto Magi]

EXCAVATOR tool

Hi All,

if you want to make CNV/CNA detection by using whole-exome sequencing data try to use the new software package EXCAVATOR. The paper has beeen recently published on Genome Biology (http://genomebiology.com/2013/14/10/R120/abstract) and the package can be downloaded at http://sourceforge.net/projects/excavatortool/.
The EXCAVATOR package combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies genomic regions into five copy number states (two-copies deletion, single-copy deletion, neutral, three-copies and multiple-copies). EXCAVATOR is a suitable tool for the investiga- tion of CNVs in large-scale projects (such as the 1000 Genomes Project and the Cancer Genome Atlas) as well as in clinical research and diagnostic activities. EXCAVATOR has been tested on the analysis of healthy individuals sequenced by the 1000 Genomes Project consortium and on the analysis of cancer samples and has been compared with other three state of the art methods (ExomeCNV, CoNIFER and XHMM).
All the comparative analyses we performed highlighted the versatility of our software and its capability of overcoming the limits and drawbacks of currently available state of the art tools.

Alberto