{"id":933,"date":"2019-05-10T08:51:51","date_gmt":"2019-05-10T08:51:51","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/icsf\/?page_id=933"},"modified":"2020-02-24T10:25:22","modified_gmt":"2020-02-24T10:25:22","slug":"plink","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/software\/applications\/plink\/","title":{"rendered":"Plink"},"content":{"rendered":"<h2>Overview<\/h2>\n<p>PLINK is a free, commonly used, open-source whole-genome association analysis toolset designed by Shaun Purcell. The software is designed flexibly to perform a wide range of basic, large-scale genetic analyses.<\/p>\n<p>Version 2.0 binaries are available on the iCSF.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>All users may access and use Plink. The software is open source. Licensed under the GNU General Public License v3<\/p>\n<p>For citation information see the <a href=\"http:\/\/bowtie-bio.sourceforge.net\/index.shtml\">Plink 2.0 website<\/a>.<\/p>\n<h2>Set up procedure<\/h2>\n<p>To use the software you will need to load the modulefile:<\/p>\n<pre class=\"\">\r\n# 1.9 beta 6.16\r\nmodule load apps\/binapps\/plink\/1.9<\/pre>\n<pre class=\"\">module load apps\/binapps\/plink\/2.0<\/pre>\n<h2>Running the application<\/h2>\n<h3>Examples<\/h3>\n<ul>\n<li><code><\/code>To verify programs is functional run the following command\n<pre>plink2 --bfile <em>inputfile<\/em> --freq --out outputfile\r\n<\/pre>\n<\/li>\n<\/ul>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"https:\/\/www.cog-genomics.org\/plink\/2.0\/\">PLINK 2.0 General Usage<\/a><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Overview PLINK is a free, commonly used, open-source whole-genome association analysis toolset designed by Shaun Purcell. The software is designed flexibly to perform a wide range of basic, large-scale genetic analyses. Version 2.0 binaries are available on the iCSF. Restrictions on use All users may access and use Plink. The software is open source. Licensed under the GNU General Public License v3 For citation information see the Plink 2.0 website. Set up procedure To use.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/software\/applications\/plink\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":7,"featured_media":0,"parent":43,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-933","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/933","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/users\/7"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/comments?post=933"}],"version-history":[{"count":7,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/933\/revisions"}],"predecessor-version":[{"id":1054,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/933\/revisions\/1054"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/43"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/media?parent=933"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}