Installation

Download

The latest stabile version of the source code is avaible as a tarball and be download here [1]

Earlier versions from here: http://popgen.dk/software/download/angsd/

Latest dev version can be found on github: https://github.com/ANGSD/angsd

The branch withhtslib now supports cram reading.

Install

Download and unpack the tarball, enter the directory and type make. Users on a mac computer, can use curl instead of wget.

Unix

The software can be compiled using make. zlib needs to be installed on your system.

wget http://popgen.dk/software/download/angsd/angsd0.615.tar.gz
tar xfz angsd0.615.tar.gz
cd angsd0.615
make
cd ..

The executable then located in angsd0.615/angsd.

NB the program also compiles a static version called angsd0.615/angsd.static which could be usefull.

Install CRAM version

To install CRAM support you also need to install htslib and can be done using the following commands

git clone https://github.com/samtools/htslib.git
git clone --branch=withhtslib git://github.com/ANGSD/angsd.git 
cd angsd
make