Open Source Genotype Compressor

The open source GVC codec is made available before scientific publication.

This pre-publication software is preliminary and may contain errors. The software is provided in good faith, but without any express or implied warranties. We refer the reader to our license.

The goal of our policy is that early release should enable the progress of science. We kindly ask to refrain from publishing analyses that were conducted using this software while its development is in progress.

Both python version 3.7 or newer and CMAKE are required. For anaconda or conda user, CMAKE, gcc and gxx libraries are required and can be installed through: conda install -c conda-forge cmake gxx_linux-64 gcc_linux-64. See requirements.txt for the list of required python libraries.

Clone this repository:

git clone https://github.com/sXperfect/gvc

Run setup script setup.sh

bash setup.sh

This step will install and compile all dependencies automatically.

In order to encode or decode the payloads based on JBIG codec, an external executable is required. You can use any of the existing and publicly available JBIG codec implementation. We provide an example on how to integrate JBIG-based codec here.

Generic compressors, such as LZMA or BZIP2, are supported. Please refer to this documentation for integration.

Compress a VCF file with default options (an example VCF file can be found in the tests folder):

python3 -m gvc encode variant_calls.vcf compressed_genotypes.gvc

A list of options can be obtained via:

python3 -m gvc encode --help

Decode a compressed VCF file with default options:

python3 -m gvc decode compressed_genotypes.gvc decoded_genotypes.txt

A list of options can be obtained via:

python3 -m gvc decode --help

For random access to a subset of compressed genotypes, additional options must be passed to the python3 -m gvc decode command:

python3 -m gvc decode --pos 1 10 --sample SAMPLE01 compressed_genotypes.gvc decoded_genotypes.txt