Best CNV software?

[dickie_ho]

Hey Adrian

I currently using excavator and I'm actually very impressed by it because it is the first program i have came across to have cross validation between my SNP array data and my Exome-data.. To top it off, it found other CNVs that were not detected on my SNP arrays and when i put my RNA-seq and smallRNA-seq data over the top its shows overlapping genes not expressed at all (where in all controls it is)...

So give that a crack and let me know how you get on... PS i work with human so i don't have a clue when it comes to anything else (so this might be useless for you)

cheers
Josh

[AdrianP]

Hello,

I know there are many reviews out there, but I can't seem to find exactly what I like.

I found this software called mrCaNaVaR, and it's great since it has it's own aligner which is supposed to be designed specifically for CNV detection. What's also great about it is that it gives .bed annotation in which it tried to determine copy number of 1kb windows regions.

What I don't like about this software is that I cannot validate the results with another aligner. If I use bwa to align the reads and then view the .bed annotations from mrCaNaVaR, I find there are regions where mrCaNaVaR says the copy number is 0 meaning no coverage, but bwa find reads that cover that position quite well.

Right now mrCaNaVaR works by quantifying copy number of windows of 1kb. It would be great if it could quantify the copy number of predefined regions such as genes for example.

Does anyone know any other software similar to mrCaNaVaR that works with NGS PE data? These are Paired-end samples. Somatic, but not human, I work on fungal pathogens, so I am sequencing spore populations.

Adrian

BioStar http://www.biostars.org/p/97688/#97692