VariantScoringFunctions

Core functions for variant scoring

Installation

Make sure you have uv installed. See here for installation instructions.

Sync Dependencies

uv sync

Setup

These annotations rely on large files of bulk reference data. These need to be constructed first.

CCREs

1. Download the CCRE bed file:

./varscore/scripts/download_ccres.sh

2. Run the following script to construct the DNATree from the CCRE bed file:

uv run python -m varscore.scripts.construct_ccre_dnatree

Variants

(Specifically, minor allele frequencies for variants)

1. Download the OpenTargets variant files

./varscore/scripts/download_variants.sh

2. Run the following script to construct the variants dataframe from the OpenTargets variant files:

uv run python -m varscore.scripts.construct_variants_df

Building Docker

Build:

docker build -t kundajelab/varscore:dev -f Dockerfile .

Sanity check to make sure it works (PLEASE DO BEFORE PUSHING):

docker run --rm kundajelab/varscore:dev varscore.ingest_model

Push:

docker push kundajelab/varscore:dev