Gnomad Rocksdb
Fast look up interface allel frequency of variants from gnomad with rocksdb.
Installation
conda install -c conda-forge python-rocksdb
pip install git+https://github.com/MuhammedHasan/gnomad_rocksdb.git
Download database
Download rocksdb for gnomad
gnomad_rocksdb_download --version {version} --db_path {output_path}
Supported version (2.1.1, 3.1.2)
Usage
from gnomad_rocksdb import GnomadMafDB
db = GnomadMafDB(db_path)
db.get('17:1000:A>C')
# 0.001
db.get('chr17:1000:A>C')
# 0.001
db['17:1000:A>C']
# 0.001
'17:1000:A>C' in db
# True
Create Database
pip install tqdm kipoiseq snakemake cython cyvcf2
# modify workflow/config.yaml
python -m snakemake -j 1