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?