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Gyper (Graph genotYPER) is a genotyper for aligned DNA sequencing data. The input files are BAM files that have been sorted and indexed (e.g. using samtools). Gyper creates a partial order graph which represent haplotypes. Currently only six HLA genes are supported: HLA-A, HLA-B, HLA-C, HLA-DQA1, HLA-DQB1, and HLA-DRB1. Gyper aligns reads from certain position of the input BAM file to the graphs and determines the individual's haplotype in a fast and accurate manner.

• Boost>=1.56.0
• SeqAn>=2.1.0 (in development)
• zlib>=1.2.8

Furthermore, Gyper is released with a CMake build system which requires CMake>=2.8.

In case you don't have CMake or zlib installed, they should be available in any package manager, e.g.

• apt-get (Ubuntu/Debian): sudo apt-get install cmake zlib
• pacman (Arch Linux): sudo pacman -S cmake zlib
• RPM (Fedora/RHEL): sudo yum install cmake zlib

Boost and SeqAn do not need to be installed, Gyper's cmake build system will automatically fetch them for you if they are missing.

Here we assume Gyper is cloned to ~/git/gyper and built in ~/git/gyper/build.

cd ~/git
git clone [email protected]:gyper/gyper.git gyper
cd gyper
mkdir build && cd build
cmake ..
make
sudo make install

The last command installs Gyper to /usr/local/bin/gyper. If you don't have root access, you can add ~/git/gyper/build/bin/gyper to your PATH environment variable manually instead.

You can specify the locations of both libraries when you use cmake, e.g.

cmake -DBOOST_INCLUDEDIR=/some/path/you/installed/boost_1_XX_0/ -DSEQAN_INCLUDE_PATH=/some/path/you/installed/seqan/include/ ..
make

If you're feeling adventurous, you can also set the BOOST_INCLUDEDIR and SEQAN_INCLUDE_PATH environment variables.