A tool for CNV discovery and genotyping from depth-of-coverage by mapped reads.
See versions of CNVnator which are available:
$ module avail root
Load and run root:
$ module load CNVnator/0.3.3 $ cnvnator
Notes from the sysadmin during installation:
$ cd /tmp $ wget https://github.com/abyzovlab/CNVnator/releases/download/v0.3.3/CNVnator_v0.3.3.zip $ unzip CNVnator_v0.3.3.zip $ module load root/6.08.06 $ cd CNVnator_v0.3.3 $ cd src/samtools $ make $ cd .. $ make $ sudo mkdir -p /export/apps/CNVnator/0.3.3 $ sudo cp cnvnator /export/apps/CNVnator/0.3.3
Note: compiled on CentOS 7 because it needs root, which in turn needs quite a bit of modern dependencies. Recommend running from compute03. Also, I compiled with max contig size of 30000, see src/HisMaker.cpp.