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MendelImpute

OpenMendel package for haplotyping and imputation

https://github.com/openmendel/mendelimpute.jl

Science Score: 77.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov
  • ✓
    Committers with academic emails
    3 of 5 committers (60.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.3%) to scientific vocabulary

Keywords from Contributors

openmendel plink snps
Last synced: 7 months ago · JSON representation ·

Repository

OpenMendel package for haplotyping and imputation

Basic Info
  • Host: GitHub
  • Owner: OpenMendel
  • License: other
  • Language: Julia
  • Default Branch: master
  • Size: 88.2 MB
Statistics
  • Stars: 26
  • Watchers: 2
  • Forks: 1
  • Open Issues: 6
  • Releases: 9
Created almost 9 years ago · Last pushed 7 months ago
Metadata Files
Readme License Citation

README.md

MendelImpute

| Documentation | Build Status | Code Coverage | |-------------------|------------------|--------------------| | | build Actions Status CI (Julia nightly) | codecov |

Installation

Download and install Julia. Within Julia, copy and paste the following: julia using Pkg pkg"add MendelImpute" This package supports Julia v1.6+.

Documentation

Example run:

The following uses data under the data/ directory.

```julia

load package & cd to data directory

using MendelImpute cd(normpath(MendelImpute.datadir()))

compress reference haplotypes from .vcf.gz to .jlso format

reffile = "ref.excludeTarget.vcf.gz" # reference VCF file tgtfile = "target.typedOnly.masked.vcf.gz" # target VCF file (GWAS file) outfile = "ref.excludeTarget.jlso" # output file name (end in .jlso) @time compress_haplotypes(reffile, tgtfile, outfile)

phase & impute (note: 2nd run will be much faster because code is compiled)

tgtfile = "target.typedOnly.masked.vcf.gz" # target VCF file (GWAS file) reffile = "ref.excludeTarget.jlso" # compressed reference file outfile = "imputed.vcf.gz" # output file name @time phase(tgtfile, reffile, outfile);

check error rate (since data was simulated)

using VCFTools Ximputed = convertgt(Float64, "imputed.vcf.gz") # imputed genotypes Xtrue = convertgt(Float64, "target.full.vcf.gz") # true genotypes m, n = size(Xtrue) # matrix dimensions error_rate = sum(Xtrue .!= Ximputed) / m / n ```

We also support PLINK binary files (.bed/.bim/.fam) via SnpArrays.jl and BGEN files .bgen via BGEN.jl.

For more realistic example, see detailed example in documentation

Bug Fixes and User support

If 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.

PRs and feature requests are welcomed!

Citation

If you use this analysis package in your research, please cite the following references in resulting publications:

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.

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.

Acknowledgement

This project has been supported by the National Institutes of Health under awards R01GM053275, R01HG006139, R25GM103774, and 1R25HG011845.

Owner

  • Name: OpenMendel
  • Login: OpenMendel
  • Kind: organization

Modern Statistical Genetics Software

Citation (CITATION.bib) 

@article{mendelimpute,
  title={{A Fast Data-Driven Method for Genotype Imputation, Phasing, and Local Ancestry Inference: MendelImpute.jl}},
  author={Chu, Benjamin B and Sobel, Eric and Wasiolek, Rory and Sinsheimer, Janet S and Zhou, Hua and Lange, Kenneth},
  journal={Bioinformatics},
  volume={37},
  number={24},
  pages={4756–4763},
  year={2021},
  publisher={Oxford University Press}
}

GitHub Events

Total
  • Watch event: 1
  • Push event: 286
  • Pull request event: 1
  • Create event: 1
Last Year
  • Watch event: 1
  • Push event: 286
  • Pull request event: 1
  • Create event: 1

Committers

Last synced: about 3 years ago

All Time
  • Total Commits: 745
  • Total Committers: 5
  • Avg Commits per committer: 149.0
  • Development Distribution Score (DDS): 0.089
Top Committers
Name Email Commits
Unknown b****9@h****m 679
Hua Zhou h****u@u****u 33
Seyoon Ko k****s@u****u 20
github-actions[bot] 4****]@u****m 11
jcpapp j****p@m****u 2
Committer Domains (Top 20 + Academic)
ucla.edu: 2 mednet.ucla.edu: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 7
  • Total pull requests: 38
  • Average time to close issues: 3 days
  • Average time to close pull requests: about 2 months
  • Total issue authors: 3
  • Total pull request authors: 3
  • Average comments per issue: 1.71
  • Average comments per pull request: 0.47
  • Merged pull requests: 17
  • Bot issues: 0
  • Bot pull requests: 34
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 1
View more stats
Top Authors
Issue Authors
  • biona001 (4)
  • kose-y (2)
  • JuliaTagBot (1)
Pull Request Authors
  • github-actions[bot] (38)
  • biona001 (3)
  • kose-y (1)
Top Labels
Issue Labels
enhancement (2)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
juliahub.com: MendelImpute

OpenMendel package for haplotyping and imputation

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 9.9%
Stargazers count: 21.4%
Average: 27.7%
Dependent packages count: 38.9%
Forks count: 40.4%
Last synced: 7 months ago

Dependencies

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