{"id":4453,"date":"2018-02-26T14:16:16","date_gmt":"2018-02-26T14:16:16","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=4453"},"modified":"2018-02-26T14:17:05","modified_gmt":"2018-02-26T14:17:05","slug":"ldsc","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/ldsc\/","title":{"rendered":"LDSC"},"content":{"rendered":"<h2>Overview<\/h2>\n<p><a href=\"https:\/\/github.com\/bulik\/ldsc\/\">LDSC<\/a> is a python package for estimating heritability and genetic correlation from GWAS summary statistics. LDSC also computes LD Scores.<\/p>\n<p>The master branch for version 1.0.0 (commit cf1707e from 02-May-17) is installed on the CSF.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>There are no restrictions on access the software on the CSF. It is release under the GNU GPL v3 <a href=\"https:\/\/github.com\/bulik\/ldsc\/blob\/master\/LICENSE\">license<\/a> so all use should adhere to that license.<\/p>\n<h2>Set up procedure<\/h2>\n<p>To access the software you must first load <em>one<\/em> of the modulefiles given below. Note that LDSC must be run with Anaconda python 2.5.0 and above. Hence one of the modulefiles below will automatically load the anaconda modulefile and one will require that you load your preferred version of anaconda before loading the LDSC modulefile.<\/p>\n<pre>\r\n# Will automatically load the Anaconda 2.5.0 (python 2.7.11) modulefile for you\r\nmodule load apps\/gcc\/python-packages\/anaconda-2.5.0\/ldsc\/1.0.0-170502\r\n\r\n# Requires that <em>you<\/em> have already loaded an Anaconda modulefile before loading this one\r\nmodule load apps\/gcc\/python-packages\/anaconda-2.5.0\/ldsc\/1.0.0-170502-any-conda\r\n<\/pre>\n<p>See below for how to run the <code>ldsc.py<\/code> script.<\/p>\n<p>The modulefiles will also set an environment variable named <code>$LDSCDIR<\/code> allowing easy access to the <code>ContinuousAnnotations<\/code> scripts in the installation:<\/p>\n<pre>\r\nls $LDSCDIR\/ContinuousAnnotations\/\r\n\r\n# Other scripts and files are available in the installation via:\r\nls $LDSCDIR\r\n<\/pre>\n<p>To see the command-line flags \/ args that the scripts require you may run the following on the login node (but no data processing should be done there):<\/p>\n<pre>\r\nldsc.py -h\r\nmunge_sumstats.py -h\r\n<\/pre>\n<h2>Running the application<\/h2>\n<p>Please do not run LDSC on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n<h3>Serial batch job submission<\/h3>\n<p>Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n<pre>\r\n#!\/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n\r\n# The LDSC main script\r\nldsc.py <em>arg1<\/em> <em>arg2<\/em> ...\r\n\r\n# Or the stats script:\r\nmunge_sumstats.py <em>arg1<\/em> <em>arg2<\/em> ...\r\n\r\n<\/pre>\n<p>Submit the jobscript using: <\/p>\n<pre>qsub <em>scriptname<\/em><\/pre>\n<p>where <em>scriptname<\/em> is the name of your jobscript.<\/p>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"https:\/\/github.com\/bulik\/ldsc\/wiki\">LDSC Wiki<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n<p>None.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Overview LDSC is a python package for estimating heritability and genetic correlation from GWAS summary statistics. LDSC also computes LD Scores. The master branch for version 1.0.0 (commit cf1707e from 02-May-17) is installed on the CSF. Restrictions on use There are no restrictions on access the software on the CSF. It is release under the GNU GPL v3 license so all use should adhere to that license. Set up procedure To access the software you.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/ldsc\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":15,"featured_media":0,"parent":31,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-4453","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4453","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/users\/15"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/comments?post=4453"}],"version-history":[{"count":2,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4453\/revisions"}],"predecessor-version":[{"id":4455,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/4453\/revisions\/4455"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/31"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/media?parent=4453"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}