This is a new version of the tool that is now being extensively benchmarked. Please note that this is a development repository. Please use the contents of this repository with caution
- plink v1.9
- bedtools
- scipy for Python3
- rpy2 for Python3
- LDSC (https://github.com/bulik/ldsc)
To run full pipeline:
python3 LSEA_2.1.py -input ./data/in.tsv \
-plink_dir <plink_folder_path> \
-bfile <.bed file for PLINK> \
-universe ./data/universe.json \
-n 100000 -m 100 -h2 0.22
To generate universe run:
python3 universe_generator.py -variants ./data/in.tsv \
-features ./data/gencode_formatted.bed \
./data/c2.all.v7.0.symbols.gmt \
-interval 100000 -o universe.json