Tools for Copy Number Variation analysis from ion Proton data.

Question

[pradyumna Jayaram]

Hello Everyone,

Can anyone suggest the tool to detection of copy number variation from the data obtained from Ampliseq exome sequencing Iontorrent proton platform. I have tried different tools like Excavator2, cnvkit, FreeC, Ionreporter. Each tool gives different region of CNV from the data.

[Titus]

I used XHMM (http://atgu.mgh.harvard.edu/xhmm/tutorial.shtml ) with Ampliseq exome sequencing Iontorrent proton platform. I had quite good result. But you need at least around 50 samples to detect bias.

[pradyumna Jayaram]

I have 10 samples and 1 pooled Control sample will it work good?

[Titus]

You can try but you will got a lot of false positive if you don't have good homogeneity in your data. Plus in Exom CNV it depends on the size of CNV you want to detect because there is part of you genome where you don't have coverage so it's an other problematic bias

Answer 1

[erwan.scaon]

You could try : https://git.unilim.fr/merilp02/CovCop

Cov’Cop is an interactive software allowing to detect CNV from amplicon sequencing data without reference samples.

And it has been tested on Ion Proton data.