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LSEA v0.2.1

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

Prerequisites

Usage

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

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