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<!doctype html><html lang=en class=no-js> <head><meta charset=utf-8><meta name=viewport content="width=device-width,initial-scale=1"><meta name=author content="Genomics Aotearoa"><link rel=icon href=/Imputation-workshop/../theme_figures/nesi_ga.png><meta name=generator content="mkdocs-1.5.3, mkdocs-material-9.5.9"><title>Genotype Imputation</title><link rel=stylesheet href=/Imputation-workshop/assets/stylesheets/main.f2e4d321.min.css><link rel=stylesheet href=/Imputation-workshop/assets/stylesheets/palette.06af60db.min.css><link rel=preconnect href=https://fonts.gstatic.com crossorigin><link rel=stylesheet href="https://fonts.googleapis.com/css?family=Mukta:300,300i,400,400i,700,700i%7CRoboto+Mono:400,400i,700,700i&display=fallback"><style>:root{--md-text-font:"Mukta";--md-code-font:"Roboto Mono"}</style><link rel=stylesheet href=/Imputation-workshop/stylesheets/extra.css><script>__md_scope=new URL("/Imputation-workshop/",location),__md_hash=e=>[...e].reduce((e,_)=>(e<<5)-e+_.charCodeAt(0),0),__md_get=(e,_=localStorage,t=__md_scope)=>JSON.parse(_.getItem(t.pathname+"."+e)),__md_set=(e,_,t=localStorage,a=__md_scope)=>{try{t.setItem(a.pathname+"."+e,JSON.stringify(_))}catch(e){}}</script></head> <body dir=ltr data-md-color-scheme=default data-md-color-primary=custom data-md-color-accent=indigo> <input class=md-toggle data-md-toggle=drawer type=checkbox id=__drawer autocomplete=off> <input class=md-toggle data-md-toggle=search type=checkbox id=__search autocomplete=off> <label class=md-overlay for=__drawer></label> <div data-md-component=skip> </div> <div data-md-component=announce> </div> <header class="md-header md-header--shadow" data-md-component=header> <nav class="md-header__inner md-grid" aria-label=Header> <a href=/Imputation-workshop/. title="Genotype Imputation" class="md-header__button md-logo" aria-label="Genotype Imputation" data-md-component=logo> <img src=/Imputation-workshop/../theme_figures/nesi_ga.png alt=logo> </a> <label class="md-header__button md-icon" for=__drawer> <svg xmlns=http://www.w3.org/2000/svg viewbox="0 0 24 24"><path d="M3 6h18v2H3V6m0 5h18v2H3v-2m0 5h18v2H3v-2Z"/></svg> </label> <div class=md-header__title data-md-component=header-title> <div class=md-header__ellipsis> <div class=md-header__topic> <span class=md-ellipsis> Genotype Imputation </span> </div> <div class=md-header__topic data-md-component=header-topic> <span class=md-ellipsis> </span> </div> </div> </div> <form class=md-header__option data-md-component=palette> <input class=md-option data-md-color-media=(prefers-color-scheme) data-md-color-scheme=default data-md-color-primary=custom data-md-color-accent=indigo aria-label="Switch to light mode" type=radio name=__palette id=__palette_0> <label class="md-header__button md-icon" title="Switch to light mode" for=__palette_1 hidden> <svg xmlns=http://www.w3.org/2000/svg viewbox="0 0 24 24"><path d="m14.3 16-.7-2h-3.2l-.7 2H7.8L11 7h2l3.2 9h-1.9M20 8.69V4h-4.69L12 .69 8.69 4H4v4.69L.69 12 4 15.31V20h4.69L12 23.31 15.31 20H20v-4.69L23.31 12 20 8.69m-9.15 3.96h2.3L12 9l-1.15 3.65Z"/></svg> </label> <input class=md-option data-md-color-media="(prefers-color-scheme: light)" data-md-color-scheme=default data-md-color-primary=custom data-md-color-accent=indigo aria-label="Switch to dark mode" type=radio name=__palette id=__palette_1> <label class="md-header__button md-icon" title="Switch to dark mode" for=__palette_2 hidden> <svg xmlns=http://www.w3.org/2000/svg viewbox="0 0 24 24"><path d="M12 8a4 4 0 0 0-4 4 4 4 0 0 0 4 4 4 4 0 0 0 4-4 4 4 0 0 0-4-4m0 10a6 6 0 0 1-6-6 6 6 0 0 1 6-6 6 6 0 0 1 6 6 6 6 0 0 1-6 6m8-9.31V4h-4.69L12 .69 8.69 4H4v4.69L.69 12 4 15.31V20h4.69L12 23.31 15.31 20H20v-4.69L23.31 12 20 8.69Z"/></svg> </label> <input class=md-option data-md-color-media="(prefers-color-scheme: dark)" data-md-color-scheme=slate data-md-color-primary=custom data-md-color-accent=indigo aria-label="Switch to system preference" type=radio name=__palette id=__palette_2> <label class="md-header__button md-icon" title="Switch to system preference" for=__palette_0 hidden> <svg xmlns=http://www.w3.org/2000/svg viewbox="0 0 24 24"><path d="M12 18c-.89 0-1.74-.2-2.5-.55C11.56 16.5 13 14.42 13 12c0-2.42-1.44-4.5-3.5-5.45C10.26 6.2 11.11 6 12 6a6 6 0 0 1 6 6 6 6 0 0 1-6 6m8-9.31V4h-4.69L12 .69 8.69 4H4v4.69L.69 12 4 15.31V20h4.69L12 23.31 15.31 20H20v-4.69L23.31 12 20 8.69Z"/></svg> </label> </form> <script>var media,input,key,value,palette=__md_get("__palette");if(palette&&palette.color){"(prefers-color-scheme)"===palette.color.media&&(media=matchMedia("(prefers-color-scheme: light)"),input=document.querySelector(media.matches?"[data-md-color-media='(prefers-color-scheme: light)']":"[data-md-color-media='(prefers-color-scheme: dark)']"),palette.color.media=input.getAttribute("data-md-color-media"),palette.color.scheme=input.getAttribute("data-md-color-scheme"),palette.color.primary=input.getAttribute("data-md-color-primary"),palette.color.accent=input.getAttribute("data-md-color-accent"));for([key,value]of Object.entries(palette.color))document.body.setAttribute("data-md-color-"+key,value)}</script> <label class="md-header__button md-icon" for=__search> <svg xmlns=http://www.w3.org/2000/svg viewbox="0 0 24 24"><path d="M9.5 3A6.5 6.5 0 0 1 16 9.5c0 1.61-.59 3.09-1.56 4.23l.27.27h.79l5 5-1.5 1.5-5-5v-.79l-.27-.27A6.516 6.516 0 0 1 9.5 16 6.5 6.5 0 0 1 3 9.5 6.5 6.5 0 0 1 9.5 3m0 2C7 5 5 7 5 9.5S7 14 9.5 14 14 12 14 9.5 12 5 9.5 5Z"/></svg> </label> <div class=md-search data-md-component=search role=dialog> <label class=md-search__overlay for=__search></label> <div class=md-search__inner role=search> <form class=md-search__form name=search> <input type=text class=md-search__input name=query aria-label=Search 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class=md-search__output> <div class=md-search__scrollwrap data-md-scrollfix> <div class=md-search-result data-md-component=search-result> <div class=md-search-result__meta> Initializing search </div> <ol class=md-search-result__list role=presentation></ol> </div> </div> </div> </div> </div> <div class=md-header__source> <a href=https://github.com/GenomicsAotearoa/Imputation-workshop title="Go to repository" class=md-source data-md-component=source> <div class="md-source__icon md-icon"> <svg xmlns=http://www.w3.org/2000/svg viewbox="0 0 448 512"><!-- Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg> </div> <div class=md-source__repository> GenomicsAotearoa/Imputation-workshop </div> </a> </div> </nav> </header> <div class=md-container data-md-component=container> <main class=md-main data-md-component=main> <div class="md-main__inner md-grid"> <div class="md-sidebar md-sidebar--primary" data-md-component=sidebar data-md-type=navigation> <div class=md-sidebar__scrollwrap> <div class=md-sidebar__inner> <nav class="md-nav md-nav--primary" aria-label=Navigation data-md-level=0> <label class=md-nav__title for=__drawer> <a href=/Imputation-workshop/. title="Genotype Imputation" class="md-nav__button md-logo" aria-label="Genotype Imputation" data-md-component=logo> <img src=/Imputation-workshop/../theme_figures/nesi_ga.png alt=logo> </a> Genotype Imputation </label> <div class=md-nav__source> <a href=https://github.com/GenomicsAotearoa/Imputation-workshop title="Go to repository" class=md-source data-md-component=source> <div class="md-source__icon md-icon"> <svg xmlns=http://www.w3.org/2000/svg viewbox="0 0 448 512"><!-- Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg> </div> <div class=md-source__repository> GenomicsAotearoa/Imputation-workshop </div> </a> </div> <ul class=md-nav__list data-md-scrollfix> <li class=md-nav__item> <a href=/Imputation-workshop/. class=md-nav__link> <span class=md-ellipsis> Home </span> </a> </li> <li class=md-nav__item> <a href=/Imputation-workshop/1_tutorial/ class=md-nav__link> <span class=md-ellipsis> Tutorial </span> </a> </li> <li class=md-nav__item> <a href=/Imputation-workshop/supplementary_1/ class=md-nav__link> <span class=md-ellipsis> Supp 1: Imputation Introduction </span> </a> </li> <li class=md-nav__item> <a href=/Imputation-workshop/supplementary_2/ class=md-nav__link> <span class=md-ellipsis> Supp 2: Sequencing Pipelines </span> </a> </li> <li class=md-nav__item> <a href=/Imputation-workshop/supplementary_3/ class=md-nav__link> <span class=md-ellipsis> Supp 3: Tutorial </span> </a> </li> <li class=md-nav__item> <a href=/Imputation-workshop/supplementary_4/ class=md-nav__link> <span class=md-ellipsis> Supp 4: Assessing Imputation Performance </span> </a> </li> <li class=md-nav__item> <a href=/Imputation-workshop/supplementary_5/ class=md-nav__link> <span class=md-ellipsis> Supp 5: Stepwise Imputation up to Sequence Level and Resource Allocation </span> </a> </li> </ul> </nav> </div> </div> </div> <div class="md-sidebar md-sidebar--secondary" data-md-component=sidebar data-md-type=toc> <div class=md-sidebar__scrollwrap> <div class=md-sidebar__inner> <nav class="md-nav md-nav--secondary" aria-label="Table of contents"> </nav> </div> </div> </div> <div class=md-content data-md-component=content> <article class="md-content__inner md-typeset"> <h1>404 - Not found</h1> </article> </div> <script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script> </div> <button type=button class="md-top md-icon" data-md-component=top hidden> <svg xmlns=http://www.w3.org/2000/svg viewbox="0 0 24 24"><path d="M13 20h-2V8l-5.5 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