{"id":21673813,"url":"https://github.com/openmendel/mendelimpute.jl","last_synced_at":"2026-02-28T19:01:47.694Z","repository":{"id":37350300,"uuid":"94558259","full_name":"OpenMendel/MendelImpute.jl","owner":"OpenMendel","description":"OpenMendel package for haplotyping and imputation","archived":false,"fork":false,"pushed_at":"2024-04-13T02:12:00.000Z","size":91359,"stargazers_count":24,"open_issues_count":3,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2024-04-14T00:57:20.638Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Julia","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/OpenMendel.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.bib","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null}},"created_at":"2017-06-16T15:40:03.000Z","updated_at":"2024-04-15T04:45:45.762Z","dependencies_parsed_at":"2024-04-15T04:55:52.472Z","dependency_job_id":null,"html_url":"https://github.com/OpenMendel/MendelImpute.jl","commit_stats":{"total_commits":745,"total_committers":5,"mean_commits":149.0,"dds":0.0885906040268456,"last_synced_commit":"9f32f0b12f1837a3f3c57f0d1c2d10168bb868cd"},"previous_names":[],"tags_count":9,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenMendel%2FMendelImpute.jl","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenMendel%2FMendelImpute.jl/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenMendel%2FMendelImpute.jl/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenMendel%2FMendelImpute.jl/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/OpenMendel","download_url":"https://codeload.github.com/OpenMendel/MendelImpute.jl/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244583162,"owners_count":20476233,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-25T13:41:24.692Z","updated_at":"2026-02-28T19:01:47.674Z","avatar_url":"https://github.com/OpenMendel.png","language":"Julia","funding_links":[],"categories":[],"sub_categories":[],"readme":"# MendelImpute\n\n| **Documentation** | **Build Status** | **Code Coverage**  |\n|-------------------|------------------|--------------------|\n| [![](https://img.shields.io/badge/docs-latest-blue.svg)](https://OpenMendel.github.io/MendelImpute.jl/dev/) [![](https://img.shields.io/badge/docs-stable-blue.svg)](https://OpenMendel.github.io/MendelImpute.jl/stable/) | [![build Actions Status](https://github.com/OpenMendel/MendelImpute.jl/workflows/CI/badge.svg)](https://github.com/OpenMendel/MendelImpute.jl/actions) [![CI (Julia nightly)](https://github.com/openmendel/mendelimpute.jl/workflows/JuliaNightly/badge.svg)](https://github.com/OpenMendel/MendelImpute.jl/actions/workflows/JuliaNightly.yml) | [![codecov](https://codecov.io/gh/OpenMendel/MendelImpute.jl/branch/master/graph/badge.svg?token=YyPqiFpIM1)](https://codecov.io/gh/OpenMendel/MendelImpute.jl) |\n\n## Installation\n\nDownload and install [Julia](https://julialang.org/downloads/). Within Julia, copy and paste the following: \n```julia\nusing Pkg\npkg\"add MendelImpute\"\n```\nThis package supports Julia `v1.6`+. \n\n## Documentation\n\n+ [**Latest**](https://OpenMendel.github.io/MendelImpute.jl/dev/)\n+ [**Stable**](https://OpenMendel.github.io/MendelImpute.jl/stable/)\n\n## Example run:\n\nThe following uses data under the `data/` directory.\n\n```julia\n# load package \u0026 cd to data directory\nusing MendelImpute\ncd(normpath(MendelImpute.datadir()))\n\n# compress reference haplotypes from .vcf.gz to .jlso format\nreffile = \"ref.excludeTarget.vcf.gz\"       # reference VCF file\ntgtfile = \"target.typedOnly.masked.vcf.gz\" # target VCF file (GWAS file)\noutfile = \"ref.excludeTarget.jlso\"         # output file name (end in .jlso)\n@time compress_haplotypes(reffile, tgtfile, outfile)\n\n# phase \u0026 impute (note: 2nd run will be much faster because code is compiled)\ntgtfile = \"target.typedOnly.masked.vcf.gz\" # target VCF file (GWAS file)\nreffile = \"ref.excludeTarget.jlso\"         # compressed reference file\noutfile = \"imputed.vcf.gz\"                 # output file name\n@time phase(tgtfile, reffile, outfile);\n\n# check error rate (since data was simulated)\nusing VCFTools\nXimputed = convert_gt(Float64, \"imputed.vcf.gz\")  # imputed genotypes\nXtrue = convert_gt(Float64, \"target.full.vcf.gz\") # true genotypes\nm, n = size(Xtrue) # matrix dimensions\nerror_rate = sum(Xtrue .!= Ximputed) / m / n\n```\n\nWe also support PLINK binary files (`.bed/.bim/.fam`) via [SnpArrays.jl](https://github.com/OpenMendel/SnpArrays.jl) and BGEN files `.bgen` via [BGEN.jl](https://github.com/OpenMendel/BGEN.jl). \n\nFor more realistic example, see [detailed example in documentation](https://openmendel.github.io/MendelImpute.jl/dev/man/Phasing_and_Imputation/#Detailed-Example)\n\n## Bug Fixes and User support\n\nIf you encounter a bug or need user support, please open a new issue on Github. Please provide as much detail as possible for bug reports, ideally a sequence of reproducible code that lead to the error. \n\nPRs and feature requests are welcomed!\n\n## Citation\n\nIf you use this analysis package in your research, please cite the following references in resulting publications:\n\n*Chu BB, Sobel EM, Wasiolek R, Ko S, Sinsheimer JS, Zhou H, Lange K. A fast Data-Driven method for genotype imputation, phasing, and local ancestry inference: MendelImpute.jl. Bioinformatics. 2021 Jul 21;37(24):4756–63. doi: 10.1093/bioinformatics/btab489. Epub ahead of print. PMID: 34289008; PMCID: [PMC8665755](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8665755/).*\n\n*Zhou H, Sinsheimer JS, Bates DM, Chu BB, German CA, Ji SS, Keys KL, Kim J, Ko S, Mosher GD, Papp JC, Sobel EM, Zhai J, Zhou JJ, Lange K. OPENMENDEL: a cooperative programming project for statistical genetics. Hum Genet. 2020 Jan;139(1):61-71. doi: 10.1007/s00439-019-02001-z. Epub 2019 Mar 26. PMID: 30915546; PMCID: [PMC6763373](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6763373/).*\n\n## Acknowledgement\n\nThis project has been supported by the National Institutes of Health under awards R01GM053275, R01HG006139, R25GM103774, and 1R25HG011845.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopenmendel%2Fmendelimpute.jl","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fopenmendel%2Fmendelimpute.jl","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopenmendel%2Fmendelimpute.jl/lists"}