Package: plinkliftover
PLINKLiftOverPLINKLiftOveris a utility enablingliftOverto work on genomics files fromPLINK,
allowing one to update the coordinates from one genome reference version to
another.InstallationPLINKLiftOver requiresPython 3.10The command line version ofliftOver,
installed and on the system pathAn appropriatechain fileTheMAP filefrom a PLINK
datasetInstall frompypipipinstall-Uplinkliftoveror install the development version withpipinstall-Ugit+https://github.com/milescsmith/plinkliftover.gitUsageplinkliftover has three subcommands:liftover: Fully convert the genomic coordinates from one version to another
in a PLINK filemap2bed: Convert a PLINK MAP file to a BED filebed2map: Convert a BED file to a MAP fileThe 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 useUCSC's online versionor you otherwise need/want a BED file.liftover:Usage:plinkliftoverliftover[OPTIONS]MAPFILECHAINFILEConvertsgenotypedatastoredinthePLINKPED+MAPformatfromonegenomebuildtoanother,usingliftOver.

Arguments:MAPFILETheplinkMAPfileto`liftOver`.[required]CHAINFILEThelocationofthechainfilestoprovideto`liftOver`.[required]Options:--pedfileTEXTOptionallyremove"unlifted SNPs"fromtheplinkPEDfileafterrunning`liftOver`.--datfileTEXTOptionallyremove'unlifted SNPs'fromadatafilecontainingalistofSNPs(e.g.for--excludeor--includein`plink`)--prefixTEXTTheprefixtogivetotheoutputfiles.--liftoverexecutableTEXTThelocationofthe`liftOver`executable.-v,--versionPrintstheversionoftheplinkliftoverpackage.--helpShowthismessageandexit.For exampleplinkliftoverliftoverupdating.maphg19ToHg38.over.chain.gz--prefixupdatedmap2bed:Usage:plinkliftovermap2bed[OPTIONS]MAPFILEConvertgenotypedatastoredinaPLINKMAPfileintoaBEDfile,allowingonetousetheonlineversionofliftOvershouldthelocalexecutableisunavailable

Arguments:MAPFILEAPLINKMAPfile.[required]Options:-o,--outputPATHLocationtosaveBEDfileto.Ifoneisnotprovided,thenitwillbesavedtowheretheMAPfileis.-v,--versionPrintstheversionoftheplinkliftoverpackage.--helpShowthismessageandexit.bed2map:Usage:plinkliftoverbed2map[OPTIONS]BEDFILEConvertgenotypedatastoredinaPLINKMAPfileintoaBEDfile,allowingonetousetheonlineversionofliftOvershouldthelocalexecutableisunavailable

Arguments:BEDFILEABEDfile.[required]Options:-o,--outputPATHLocationtosaveMAPfileto.Ifoneisnotprovided,thenitwillbesavedtowheretheBEDfileis.-v,--versionPrintstheversionoftheplinkliftoverpackage.--helpShowthismessageandexit.Note!By default,PLINK 2.0does not
use/create the required MAP file.  It can be generated using PLINK 1.9 byplink--bfileoriginal--recode--outto_updatewhereoriginalis the prefix for the bed/bim/fam files andto_updateis the prefix to give the new files.🛡 LicenseThis project is licensed under the terms of theGNU GPL v3.0license. SeeLICENSEfor more details.📃 Citation@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}}
}CreditsThis project was generated withpython-package-template.