ANGSD: Analysis of next generation Sequencing Data

Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.

Installation

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Download and Installation

To download and use ANGSD you need to download the htslib and the angsd source folder

You can either download the angsd0.902.tar.gz which contains both. [1]

Or you can use github for the latest version of both htslib and angsd

Earlier versions from here: http://popgen.dk/software/download/angsd/ And here: https://github.com/ANGSD/angsd/releases

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/angsd0.902.tar.gz
tar xfz angsd0.902.tar.gz
cd htsdir;make;cd ..
cd angsd
make HTSSRC=../htsdir
cd ..

The executable then located in angsd/angsd.

Install from github

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 https://github.com/ANGSD/angsd.git 
cd htsdir;make;cd ../angsd ;make HTSSRC=../htsdir
make