Compile SHAPEIT5

Table of contents

1. Compile SHAPEIT5

Compile SHAPEIT5

Download the last version of the SHAPEIT5 code using:

git clone --recurse-submodules https://github.com/odelaneau/shapeit5.git

Adding --recurse-submodules allows cloning automatically the xcftools submodule required by shapeit5.

Navigate to the downloaded folder using cd shapeit5.

You’ll find there a folder containing all the software packages are other utility folders:

• docker: all scripts needed to build a docker file comprising all binaries
• docs: documentation in html
• ligate: ligate multiple phased BCF/VCF files into a chromosome length file
• phase_common: phase common sites, typically SNP array data
• phase_rare: phase rare variants onto a scaffold of common variants
• resources: genetics maps [b37/b38] and coordinates for [5/20] cM chunks
• static_bins: static binaries of all executables
• switch: compute switch error rate and genotyping error rate given simulated or trio data
• tasks: scripts used to phase large datasets, good base to start pipelining
• test: simulated data for first-step testing of the method
• versions: versioning
• xcftools: tool to handle XCF file format

Each software in the suite contains the same folder structure:

• bin: folder for the compiled binary.
• obj: folder with all binary objects.
• src: folder with source code.
• makefile: Makefile to compile the program.

In order to compile a specific tool, for example phase_rare, go in directory of the software (cd phase_rare) and edit the specific makefile at lines so that the following variables are correctly set up (look at the paths already there for an example):

• HTSSRC: path to the root of the HTSlib library, the prefix for HTSLIB_INC and HTSLIB_LIB paths.
• HTSLIB_INC: path to the HTSlib header files.
• HTSLIB_LIB: path to the static HTSlib library (file libhts.a).
• BOOST_INC: path to the BOOST header files (usually /usr/include).
• BOOST_LIB_IO: path to the static BOOST iostreams library (file libboost_iostreams.a).
• BOOST_LIB_PO: path to the static BOOST program_options library (file libboost_program_options.a).

If installed at the system level, static libraries (*.a files) can be located with this command:

locate libboost_program_options.a libboost_iostreams.a libhts.a

Once all paths correctly set up, proceed with the compilation using make. The binary can be found in the bin/ folder of each tool and will have a name similar to SHAPEIT5_phase_common. You will need to copy the modified makefile in each tool (folder) of SHAPEIT5.