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.