CNV calling program for NGS data that can be down-scaled for reads covering one gene

Question

[zedmunds]

Hi, I am looking for an appropriate CNV calling program for next generation sequence data. My issue is there are so many out there with so many different parameters, every time I think I found one that will work, one of my requirements is missing. It appears that most of the CNV calling programs seem to only be applicable to whole genomes or whole exomes. I am looking for a program that will work for coverage of only one gene, or a program that can be down-scaled to this size.

My other requirements include:

• a Windows or Linux platform (if not platform-independent)
• written in either Perl, R or Java
• requires bam files as input
• and that it is free

I am really new to this kind of thing so any help is appreciated.

Thank you!

Answer 1

[mikhail.shugay]

Hello! This review (http://www.ncbi.nlm.nih.gov/pubmed/24599115) could answer your question, see picture below. If you need to "scale to a single gene" the simplest way is to add all your tracks to IGV or UCSC GB and look at your gene directly :)

[zedmunds]

Thank you for the help, I will definitely check out those algorithms. One of the issues I forgot to mention is that when I view my tracks in IGV, it does not detect some of the variants I am looking for (like an 84bp deletion) in samples that I know contain this variant.

[mikhail.shugay]

Ok, but what software were you using to get your CNV profile? If you have some specific gene of interest, maybe it will worth to try all suitable software and just select the best one based on your control data? I know this sounds quite obvious, but I don't think there is an universal software.

Answer 2

[Kizuna]

I would give ExomeDepth a try.. it meets your requirements.. and many users have tried it so you can find some useful documentation..

Hope this might help,

Kiz