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Plink LiftOver Python Script

Overview

This Python script facilitates lifting of genetic data files (Plink format MAP, PED) from one Human genome build version to another using the liftOver tool . It can liftover from easily between multiple builds available. E.g Hg19, Hg18, GRCH36 and others.

wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver
export PATH=$PATH:/~liftOver PATH

The script converts input files to BED format, performs lifting, and converts back to the original format, providing a seamless transition between genome versions.

Usage

python liftover_python_umich_update.py -m old.map -p old.ped -c chain_file -o new.prefix

Arguments

• -m, --map: Input MAP file containing genetic marker information (required).
• -p, --ped: Input PED file containing genotype information (optional).
• -- CHAIN: Liftover Chain File.
• -o, --prefix: Prefix for output files (required).
• --LIFTOVER_BIN: Lifover Binaries.

Functions

1. usage(): Prints the usage information of the script.
2. die(msg): Prints error message and exits the script.
3. myopen(fn): Opens a file and handles gzip format if applicable.
4. map2bed(fin, fout): Converts MAP file to BED format.
5. liftBed(fin, fout, unlifted): Lifts BED file using liftOver tool.
6. bed2map(fin, fout): Converts BED file back to MAP format.
7. liftPed(fin, fout, fOldMap): Lifts PED file.

Execution

• The script parses command-line arguments.
• Converts MAP to BED format.
• Performs lifting using liftOver.
• LIFTOVER_BIN

$ wget https://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver
$ chmod +x ./filePath/liftOver
$ ./filePath/liftOver

• Converts lifted files back to original formats.

Dependencies

• Ensure that the liftOver tool is installed and accessible in the system path.
• Ensure that you get the appropriate chain file (that conversts one build to another) from https://hgdownload2.soe.ucsc.edu/downloads.html
• Plink genotype files can be recoded from binary (bed, bim and fam) to text (map and ped) formats

plink --bfile {prefix} --recode --out {output_file_name}

To re-obtain binary formats we do:

plink --file {} --recode --make-bed --out {output_file_name}