This repository contains hail scripts designed to import, analyse and execute sample_qc and variant_qc on a collection of data cohorts at the Sanger Institute. The scripts are adapted from the gnomad sample and variant QC v2 and v3 analysis. (https://github.com/broadinstitute/gnomad_qc/blob/master/gnomad_qc/v2/ , https://github.com/broadinstitute/gnomad_qc/tree/master/gnomad_qc/v3).
Please visit https://confluence.sanger.ac.uk/display/HGI/WSI+Exome+Joint+Call for more information on the order of running the scripts, code snippets and results. Please contact Pavlos (pa10) for any questions.
Spark Cluster with hail installed. To obtain the code please type:
mkdir gnomad_sanger_cohorts
git init
git pull