olavurmortensen / fargen-1-exome

FarGen Phase I Exome

FIXME: Once the paper is published, include reference and DOI in this README.

This repository contains code to reproduce the following paper:

FIXME: insert reference here.

Corresponding author for the paper: [e-mail]

The notebooks that produce the results for the paper can be found in notebooks/main/. Pre-processing of gnomAD data, as well as merging, can be found in notebooks/gnomad_exome_sites/ and notebooks/gnomad_genome_genotypes/. Additionally, some genealogical analyses are found in the genealogy/ folder.

Setup

Dependencies are defined in env.yml. These can be installed using Conda, as follows:

conda env create -f env.yml

Note that there is a separate setup procedure in the genealogy/ folder.

Input data

The data analysed in the project was processed by the LinkSeq pipeline. For more information about this, see the LinkSeq repository and the paper referenced above.