angsd:

===== Program for analysing NGS data.

http://www.popgen.dk/angsd

Installation:

1. Using a local folder containing htslib

#download htslib
git clone --recurse-submodules https://github.com/samtools/htslib.git;
#download angsd
git clone https://github.com/angsd/angsd.git;

#install htslib
cd htslib
make

#install angsd
cd ../angsd
make HTSSRC=../htslib

2. Systemwide installation of htslib

git clone https://github.com/angsd/angsd.git;
cd angsd; make HTSSRC=systemwide

3. Using htslib submodule

git clone https://github.com/angsd/angsd.git;
cd angsd; make

Notes

• I've switched over to using htslib for parsing single reads (to allow for CRAM reading, while avoid having to write my own CRAM parser). I'm still using my own readpools. Users should therefore also download and install htslib.
• If you are on a mac computer and the compilation process complains about a missnig crybtolib library then do 'make CRYPTOLIB=""'

Program has a paper

http://www.biomedcentral.com/1471-2105/15/356/abstract