Fast look up interface and prediction for missing variants in look table for spliceAI with rocksdb.
Clone this git repository:
git clone https://github.com/gagneurlab/spliceai_rocksdb.git
Go to the cloned repository:
cd spliceai_rocksdb
Create conda environment:
# Recommended if you have mamba installed
mamba env create -f environment.yml
# otherwise
conda env create -f environment.yml
Activate conda environment:
conda activate spliceai-rocksdb
Install modules from spliceai_rocksdb
pip install -e .
Download rocksdb for gnomad
spliceai_rocksdb_download --version {version} --db_path {output_path}
Supported version (grch37, grch38)
To run spliceai_rocksdb in the command line use:
spliceai_rocksdb -I input.vcf -O output.[csv, parquet, vcf] -R genome.fa -A grch37 -db {db_path}
Alternatively use the snakemake pipeline in /workflow
cd workflow
# modify config.yaml and setup datasets
python -m snakemake -j 1