Wanying-Zhu/liftover_py

Liftover_py

This is a python wrapper of UCSC liftover tool. Commandline tool liftover_py can take PLINK .bim file or other text input, run liftover and return converted output follow the original format.

Prerequisites

1. LiftOver must be installed/downloaded. Check LiftOver executable on UCSC genome browser website.
2. Input file can be PLINK .bim or general text file, must uses tab as delimiters
3. Now only commandline version of liftover_py is avaialable.

Example code

# --chr_id_pos is not needed if input file is PLINK .bim format
python formatting_plink_bim_to_UCSC_bed.py \
--input input_file \
--output output_file \
--output_path ./inputs \
--chain_file hg19ToHg38.over.chain.gz \
--liftover ./liftOver \
--chr_id_pos 0:1:2