plinkliftover 0.2.0

Converts genotype data stored in plink's PED+MAP format from one genome build to another, using liftOver

PLINKLiftOver

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.

## Installation

PLINKLiftOver requires

• Python 3.8
• The command line version of liftOver, installed and on the system path
• An appropriate chain file
• The MAP file from a PLINK dataset

pip install -U plinkliftover

or install with the development version with

pip install -U git+https://github.com/milescsmith/plinkliftover.git

Usage

Usage: plinkliftover [OPTIONS] MAPFILE CHAINFILE

  Converts genotype data stored in plink's 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 updating.map hg19ToHg38.over.chain.gz

Note!

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.

🛡 License

This project is licensed under the terms of the GNU GPL v3.0 license. See LICENSE for more details.

📃 Citation

@misc{plinkliftover,
  author = {Miles Smith <[e-mail]>},
  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}}
}

Credits

This project was generated with python-package-template.