This repo contains code that is relevant for the analysis (Mapping, BAM qc, Variant Calling, Filtering etc...) of IGSR data
APACHE-2.0 License
This repo contains code that is relevant for the analysis (Mapping, BAM qc, Variant Calling, Filtering etc...) of IGSR data
The International Genome Sample Resource (IGSR) is a project funded by the Wellcome Trust created after the finalization of the 1000 Genomes Project in order to maintain and expand the resource. It has the following aims:
This repository contains code used in the different analyses pipelines that we use in the project. To use this code please follow the steps described below
Modify your $PYTHONPATH to include the required libraries:
export PYTHONPATH=${ehive_dir}/wrappers/python3/:$PYTHONPATH
Modify your $PERL5LIB to include the required libraries:
export PERL5LIB=${ehive_dir}/modules/:${igsr_analysis_dir}/:${PERL5LIB}
Modify your $PATH to include the location of the eHive scripts:
export PATH=${ehive_dir}/scripts/:${PATH}
pip install igsr_analysis
And you are ready to go!
${igsr_analysis_dir}
is the folder where you have cloned https://github.com/igsr/igsr_analysis.git
${ehive_dir}
is the folder where you have cloned https://github.com/Ensembl/ensembl-hive.git