PLINKLiftOver is a utility enabling liftOver to work on genomics files from PLINK, allowing one to update the coordinates from one genome reference version to another.
PLINKLiftOver requires
- Python 3.10
- The command line version of liftOver, installed and on the system path
- An appropriate chain file
- The MAP file from a PLINK dataset
Install from pypi
pip install -U plinkliftover
or install the development version with
pip install -U git+https://github.com/milescsmith/plinkliftover.git
plinkliftover has three subcommands:
- liftover: Fully convert the genomic coordinates from one version to another in a PLINK file
- map2bed: Convert a PLINK MAP file to a BED file
- bed2map: Convert a BED file to a MAP file
The latter two subcommands are most useful in situations where it is not possible to run the liftOver executable locally (i.e. you are on Windows) but can use UCSC's online version or you otherwise need/want a BED file.
Usage: plinkliftover liftover [OPTIONS] MAPFILE CHAINFILE
Converts genotype data stored in the PLINK PED+MAP format from one genome
build to another, using liftOver.
Arguments:
MAPFILE The plink MAP file to `liftOver`. [required]
CHAINFILE The location of the chain files to provide to `liftOver`.
[required]
Options:
--pedfile TEXT Optionally remove "unlifted SNPs" from the plink
PED file after running `liftOver`.
--datfile TEXT Optionally remove 'unlifted SNPs' from a data
file containing a list of SNPs (e.g. for
--exclude or --include in `plink`)
--prefix TEXT The prefix to give to the output files.
--liftoverexecutable TEXT The location of the `liftOver` executable.
-v, --version Prints the version of the plinkliftover package.
--help Show this message and exit.
For example
plinkliftover liftover updating.map hg19ToHg38.over.chain.gz --prefix updated
Usage: plinkliftover map2bed [OPTIONS] MAPFILE
Convert genotype data stored in a PLINK MAP file into a BED file, allowing
one to use the online version of liftOver should the local executable is
unavailable
Arguments:
MAPFILE A PLINK MAP file. [required]
Options:
-o, --output PATH Location to save BED file to. If one is not provided,
then it will be saved to where the MAP file is.
-v, --version Prints the version of the plinkliftover package.
--help Show this message and exit.
Usage: plinkliftover bed2map [OPTIONS] BEDFILE
Convert genotype data stored in a PLINK MAP file into a BED file, allowing
one to use the online version of liftOver should the local executable is
unavailable
Arguments:
BEDFILE A BED file. [required]
Options:
-o, --output PATH Location to save MAP file to. If one is not provided,
then it will be saved to where the BED file is.
-v, --version Prints the version of the plinkliftover package.
--help Show this message and exit.
By default, PLINK 2.0 does not use/create the required MAP file. It can be generated using PLINK 1.9 by
plink --bfile original --recode --out to_update
where original
is the prefix for the bed/bim/fam files and to_update
is the prefix to give the new files.
This project is licensed under the terms of the GNU GPL v3.0
license. See LICENSE for more details.
@misc{plinkliftover,
author = {Miles Smith <miles-smith@omrf.org>},
title = {Awesome `plinkliftover` is a Python cli/package created with https://github.com/TezRomacH/python-package-template},
year = {2021},
publisher = {GitHub},
journal = {GitHub repository},
howpublished = {\url{https://github.com/milescsmith/plinkliftover}}
}
This project was generated with python-package-template
.