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| <html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Home · VCFTools</title><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="assets/documenter.js"></script><script src="siteinfo.js"></script><script src="../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href>VCFTools</a></span></div><form class="docs-search" action="search/"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li class="is-active"><a class="tocitem" href>Home</a><ul class="internal"><li><a class="tocitem" href="#Package-Features"><span>Package Features</span></a></li><li><a class="tocitem" href="#Installation"><span>Installation</span></a></li><li><a class="tocitem" href="#Manual-Outline"><span>Manual Outline</span></a></li></ul></li><li><a class="tocitem" href="man/summaryinfo/">VCF Summary</a></li><li><a class="tocitem" href="man/filter/">Filter</a></li><li><a class="tocitem" href="man/convert/">Convert</a></li><li><a class="tocitem" href="man/write/">Write</a></li><li><a class="tocitem" href="man/conformgt/">Match markers in two VCF</a></li><li><a class="tocitem" href="man/grm/">Genetic Relationship Matrix</a></li><li><a class="tocitem" href="man/aim/">Ancestry informative markers</a></li><li><a class="tocitem" href="man/api/">API</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Home</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Home</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com/OpenMendel/VCFTools.jl/blob/master/docs/src/index.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="VCFTools.jl"><a class="docs-heading-anchor" href="#VCFTools.jl">VCFTools.jl</a><a id="VCFTools.jl-1"></a><a class="docs-heading-anchor-permalink" href="#VCFTools.jl" title="Permalink"></a></h1><p><em>Julia utilities for handling VCF files</em></p><p><code>VCFTools.jl</code> implements some Julia utilities for handling <a href="https://github.com/samtools/hts-specs">VCF</a> files. This package heavily uses the VCF parser developed in the <a href="https://github.com/BioJulia/GeneticVariation.jl"><code>BioJulia/GeneticVariation.jl</code></a> package, which has been superseded by <a href="https://github.com/rasmushenningsson/VariantCallFormat.jl"><code>VariantCallFormal.jl</code></a></p><h2 id="Package-Features"><a class="docs-heading-anchor" href="#Package-Features">Package Features</a><a id="Package-Features-1"></a><a class="docs-heading-anchor-permalink" href="#Package-Features" title="Permalink"></a></h2><ul><li>Calculate genotype statistics (minor allele frequencies, minor allele, count of missing genotypes, etc) from a VCF file. </li><li>Extract specific data fields from a VCF file. </li><li>Filtering/subsetting VCF files. </li><li>Match markers in two VCF files according to ID. </li><li>Calculation of Genetic Relationship Matrix.</li><li>Rank SNPs by their ancestry informativeness.</li><li>Saving numeric matrix into VCF file</li></ul><h2 id="Installation"><a class="docs-heading-anchor" href="#Installation">Installation</a><a id="Installation-1"></a><a class="docs-heading-anchor-permalink" href="#Installation" title="Permalink"></a></h2><p>Within Julia,</p><pre><code class="language-julia hljs">using Pkg | ||
| pkg"add VCFTools"</code></pre><p>This package supports Julia <code>v1.5</code>+.</p><h2 id="Manual-Outline"><a class="docs-heading-anchor" href="#Manual-Outline">Manual Outline</a><a id="Manual-Outline-1"></a><a class="docs-heading-anchor-permalink" href="#Manual-Outline" title="Permalink"></a></h2><ul><li><a href="#VCFTools.jl">VCFTools.jl</a></li><li class="no-marker"><ul><li><a href="#Package-Features">Package Features</a></li><li><a href="#Installation">Installation</a></li><li><a href="#Manual-Outline">Manual Outline</a></li></ul></li><li><a href="man/aim/#Ancestry-Informative-Markers">Ancestry Informative Markers</a></li><li class="no-marker"><ul><li><a href="man/aim/#Example-data">Example data</a></li><li><a href="man/aim/#Preprocess-data">Preprocess data</a></li><li><a href="man/aim/#Run-AIM-selection">Run AIM selection</a></li></ul></li><li><a href="man/api/#API">API</a></li><li class="no-marker"><ul><li><a href="man/api/#Index">Index</a></li><li><a href="man/api/#Functions">Functions</a></li></ul></li><li><a href="man/conformgt/#Match-markers-in-two-VCF-files">Match markers in two VCF files</a></li><li class="no-marker"><ul><li><a href="man/conformgt/#Example-files">Example files</a></li><li><a href="man/conformgt/#Match-markers-according-to-ID">Match markers according to ID</a></li><li><a href="man/conformgt/#Match-markers-according-to-position">Match markers according to position</a></li></ul></li><li><a href="man/convert/#Convert-genotype/haplotype/dosage-to-numeric-arrays">Convert genotype/haplotype/dosage to numeric arrays</a></li><li class="no-marker"><ul><li><a href="man/convert/#Example-VCF-file">Example VCF file</a></li><li><a href="man/convert/#Genetic-model">Genetic model</a></li><li><a href="man/convert/#Convert-GT-data-into-a-numeric-genotype-matrix">Convert GT data into a numeric genotype matrix</a></li><li><a href="man/convert/#Convert-GT-data-into-haplotypes-panels">Convert GT data into haplotypes panels</a></li><li><a href="man/convert/#Convert-DS-data-into-dosages">Convert DS data into dosages</a></li><li><a href="man/convert/#Extract-data-marker-by-maker-or-window-by-window">Extract data marker-by-maker or window-by-window</a></li><li><a href="man/convert/#Sample-ID,-Chromosome,-SNP-position,-REF/ALT-alleles">Sample ID, Chromosome, SNP position, REF/ALT alleles</a></li></ul></li><li><a href="man/filter/#Filter-data-fields-in-a-VCF-file">Filter data fields in a VCF file</a></li><li class="no-marker"><ul><li><a href="man/filter/#Example-VCF-file">Example VCF file</a></li><li><a href="man/filter/#Extract-a-single-field">Extract a single field</a></li><li><a href="man/filter/#Extract-more-than-one-fields">Extract more than one fields</a></li><li><a href="man/filter/#No-found-data-fields">No found data fields</a></li><li><a href="man/filter/#Subsetting-VCF-files-using-array-masks">Subsetting VCF files using array masks</a></li><li><a href="man/filter/#Filter-by-chromosome">Filter by chromosome</a></li><li><a href="man/filter/#Masking-entries-of-a-VCF-files">Masking entries of a VCF files</a></li></ul></li><li><a href="man/grm/#Genetic-Relationship-Matrix">Genetic Relationship Matrix</a></li><li class="no-marker"><ul><li><a href="man/grm/#Example-data">Example data</a></li><li><a href="man/grm/#High-proportion-of-missing-data">High proportion of missing data</a></li><li><a href="man/grm/#Inhomogeneous-populations">Inhomogeneous populations</a></li></ul></li><li><a href="man/summaryinfo/#VCF-summary-information">VCF summary information</a></li><li class="no-marker"><ul><li><a href="man/summaryinfo/#Example-VCF-file">Example VCF file</a></li><li><a href="man/summaryinfo/#Summary-statistics">Summary statistics</a></li></ul></li><li><a href="man/write/#Write">Write</a></li><li class="no-marker"><ul><li><a href="man/write/#Phased-genotypes">Phased genotypes</a></li><li><a href="man/write/#Unphased-genotypes">Unphased genotypes</a></li></ul></li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="man/summaryinfo/">VCF Summary »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Monday 4 September 2023 02:09">Monday 4 September 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html> | ||
| pkg"add VCFTools"</code></pre><p>This package supports Julia <code>v1.5</code>+.</p><h2 id="Manual-Outline"><a class="docs-heading-anchor" href="#Manual-Outline">Manual Outline</a><a id="Manual-Outline-1"></a><a class="docs-heading-anchor-permalink" href="#Manual-Outline" title="Permalink"></a></h2><ul><li><a href="#VCFTools.jl">VCFTools.jl</a></li><li class="no-marker"><ul><li><a href="#Package-Features">Package Features</a></li><li><a href="#Installation">Installation</a></li><li><a href="#Manual-Outline">Manual Outline</a></li></ul></li><li><a href="man/aim/#Ancestry-Informative-Markers">Ancestry Informative Markers</a></li><li class="no-marker"><ul><li><a href="man/aim/#Example-data">Example data</a></li><li><a href="man/aim/#Preprocess-data">Preprocess data</a></li><li><a href="man/aim/#Run-AIM-selection">Run AIM selection</a></li></ul></li><li><a href="man/api/#API">API</a></li><li class="no-marker"><ul><li><a href="man/api/#Index">Index</a></li><li><a href="man/api/#Functions">Functions</a></li></ul></li><li><a href="man/conformgt/#Match-markers-in-two-VCF-files">Match markers in two VCF files</a></li><li class="no-marker"><ul><li><a href="man/conformgt/#Example-files">Example files</a></li><li><a href="man/conformgt/#Match-markers-according-to-ID">Match markers according to ID</a></li><li><a href="man/conformgt/#Match-markers-according-to-position">Match markers according to position</a></li></ul></li><li><a href="man/convert/#Convert-genotype/haplotype/dosage-to-numeric-arrays">Convert genotype/haplotype/dosage to numeric arrays</a></li><li class="no-marker"><ul><li><a href="man/convert/#Example-VCF-file">Example VCF file</a></li><li><a href="man/convert/#Genetic-model">Genetic model</a></li><li><a href="man/convert/#Convert-GT-data-into-a-numeric-genotype-matrix">Convert GT data into a numeric genotype matrix</a></li><li><a href="man/convert/#Convert-GT-data-into-haplotypes-panels">Convert GT data into haplotypes panels</a></li><li><a href="man/convert/#Convert-DS-data-into-dosages">Convert DS data into dosages</a></li><li><a href="man/convert/#Extract-data-marker-by-maker-or-window-by-window">Extract data marker-by-maker or window-by-window</a></li><li><a href="man/convert/#Sample-ID,-Chromosome,-SNP-position,-REF/ALT-alleles">Sample ID, Chromosome, SNP position, REF/ALT alleles</a></li></ul></li><li><a href="man/filter/#Filter-data-fields-in-a-VCF-file">Filter data fields in a VCF file</a></li><li class="no-marker"><ul><li><a href="man/filter/#Example-VCF-file">Example VCF file</a></li><li><a href="man/filter/#Extract-a-single-field">Extract a single field</a></li><li><a href="man/filter/#Extract-more-than-one-fields">Extract more than one fields</a></li><li><a href="man/filter/#No-found-data-fields">No found data fields</a></li><li><a href="man/filter/#Subsetting-VCF-files-using-array-masks">Subsetting VCF files using array masks</a></li><li><a href="man/filter/#Filter-by-chromosome">Filter by chromosome</a></li><li><a href="man/filter/#Masking-entries-of-a-VCF-files">Masking entries of a VCF files</a></li></ul></li><li><a href="man/grm/#Genetic-Relationship-Matrix">Genetic Relationship Matrix</a></li><li class="no-marker"><ul><li><a href="man/grm/#Example-data">Example data</a></li><li><a href="man/grm/#High-proportion-of-missing-data">High proportion of missing data</a></li><li><a href="man/grm/#Inhomogeneous-populations">Inhomogeneous populations</a></li></ul></li><li><a href="man/summaryinfo/#VCF-summary-information">VCF summary information</a></li><li class="no-marker"><ul><li><a href="man/summaryinfo/#Example-VCF-file">Example VCF file</a></li><li><a href="man/summaryinfo/#Summary-statistics">Summary statistics</a></li></ul></li><li><a href="man/write/#Write">Write</a></li><li class="no-marker"><ul><li><a href="man/write/#Phased-genotypes">Phased genotypes</a></li><li><a href="man/write/#Unphased-genotypes">Unphased genotypes</a></li></ul></li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="man/summaryinfo/">VCF Summary »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Tuesday 5 September 2023 02:09">Tuesday 5 September 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html> |
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