Analyzes multiple biases in read coverage to detect CNVs in NGS data. To overcome a typical weakness of read depth (RD) methods, GROM-RD employs a CNV search using size-varying overlapping windows to improve breakpoint resolution. GROM-RD was able to improve RD sensitivity, specificity, and breakpoint accuracy compared to CNVnator and RDXplorer, the two most frequently used RD algorithms. Additionally, GROM-RD had a short run time that was relatively insensitive to read coverage indicating excellent scalability of the method for different datasets.

• Version: 1.0
• Added: May, 2017
• Link: http://grigoriev.rutgers.edu/software/grom-rd/index.html

See which versions of grom-rd are available:

$ module avail grom-rd

Load groovy

$ module load grom-rd/1.0

Notes from the sysadmin during installation:

$ cd /tmp
$ wget http://grigoriev.rutgers.edu/software/grom-rd/GROM-RD_v1.0.tar.gz
$ tar xf GROM-RD_v1.0.tar.gz
$ cd GROM-RD_v1.0
$ make
$ sudo mkdir -p /export/apps/grom-rd/1.0
$ sudo cp bin/GROM-RD  /export/apps/grom-rd/1.0