{"id":4474,"date":"2020-02-03T15:46:05","date_gmt":"2020-02-03T15:46:05","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=4474"},"modified":"2020-02-03T15:48:08","modified_gmt":"2020-02-03T15:48:08","slug":"snptest","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/snptest\/","title":{"rendered":"SNPTest"},"content":{"rendered":"<h2>Overview<\/h2>\n<p>SNPTest\u00a0is a program for the analysis of single SNP association in genome-wide studies. The tests implemented include<\/p>\n<p>Binary (case-control) phenotypes, single and multiple quantitative phenotypes<br \/>\nBayesian and Frequentist tests<br \/>\nAbility to condition upon an arbitrary set of covariates and\/or SNPs.<br \/>\nVarious different methods for the dealing with imputed SNPs.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>All users may access and use SNPTest. The software is (c) 2007, The University of Oxford.<\/p>\n<h2>Running the application<\/h2>\n<p>Please do not run SNPTest commands on the login node. qrsh is recommended for some commands. Computationally intense work should be done via the batch system.<\/p>\n<h3>Examples<\/h3>\n<p>The following example first runs <code>SNPTest<\/code> as a serial job.<\/p>\n<pre>#!\/bin\/bash --login\r\n#$ -S \/bin\/bash\r\n#$ -cwd\r\nmodule load apps\/binapps\/snptest\/2.5.2\r\n\r\nsnptest \\\r\n<span class=\"example_option\">-summary_stats_only<\/span>\u00a0\\\r\n<span class=\"example_option\">-data<\/span>\u00a0$SNPTESTDIR\/example\/cohort1.gen $SNPTESTDIR\/example\/cohort1.sample $SNPTESTDIR\/example\/cohort2.gen $SNPTESTDIR\/example\/cohort2.sample \\\r\n<span class=\"example_option\">-o<\/span>\u00a0ex.out\r\n<\/pre>\n<p>and submit the job using <code>qsub <em>jobscript<\/em><\/code> where jobscript is the name of your job script file.<\/p>\n<h2>Further info<\/h2>\n<ul>\n<li style=\"list-style-type: none;\">\n<ul>\n<li><a href=\"https:\/\/mathgen.stats.ox.ac.uk\/genetics_software\/snptest\/snptest.html#frequentist_tests\">SNPTest Manual<\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Overview SNPTest\u00a0is a program for the analysis of single SNP association in genome-wide studies. The tests implemented include Binary (case-control) phenotypes, single and multiple quantitative phenotypes Bayesian and Frequentist tests Ability to condition upon an arbitrary set of covariates and\/or SNPs. Various different methods for the dealing with imputed SNPs. Restrictions on use All users may access and use SNPTest. The software is (c) 2007, The University of Oxford. Running the application Please do not.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/snptest\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":7,"featured_media":0,"parent":33,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-4474","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4474","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/users\/7"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/comments?post=4474"}],"version-history":[{"count":3,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4474\/revisions"}],"predecessor-version":[{"id":4477,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/4474\/revisions\/4477"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/pages\/33"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/wp-json\/wp\/v2\/media?parent=4474"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}