sanger_gnomad_hail_qc

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.

Requirements

Spark Cluster with hail installed. To obtain the code please type:

mkdir gnomad_sanger_cohorts
git init
git pull

Name		Name	Last commit message	Last commit date
Latest commit History 1,025 Commits
analysis_files		analysis_files
hail_configuration_files @ 69ba5da		hail_configuration_files @ 69ba5da
import_data		import_data
notebooks		notebooks
plots		plots
sample_qc_v3		sample_qc_v3
v2_based_code/sample_qc		v2_based_code/sample_qc
variant_qc		variant_qc
.gitignore		.gitignore
.gitmodules		.gitmodules
README.md		README.md
hail_functions.py		hail_functions.py
kousik_filter.py		kousik_filter.py
non_ref_counts.py		non_ref_counts.py
references.py		references.py