Table of Contents

CNVnator

A tool for CNV discovery and genotyping from depth-of-coverage by mapped reads.

Information

Usage

See versions of CNVnator which are available: 

$ module avail root

Load and run root: 

$ module load CNVnator/0.3.3
$ cnvnator

Installation

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.