{"id":1240,"date":"2014-01-20T10:38:31","date_gmt":"2014-01-20T10:38:31","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=1240"},"modified":"2017-01-25T11:33:57","modified_gmt":"2017-01-25T11:33:57","slug":"vcftools","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/vcftools\/","title":{"rendered":"VCFtools"},"content":{"rendered":"<h2>Overview<\/h2>\n<p>VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide methods for working with VCF files: validating, merging, comparing and calculate some basic population genetic statistics.<\/p>\n<p>Version 0.1.14 is installed on the CSF. It was compiled with gcc 4.9.0. There is a version 0.1.14 which uses zlib 1.2.8 which may give better performance.<\/p>\n<p>Version 0.1.11 is also installed on the CSF. It was compiled with gcc 4.7.0.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>The software is open source. All CSF users may access it.<\/p>\n<h2>Set up procedure<\/h2>\n<p>To access the software you must first load the appropriate modulefile:<\/p>\n<pre>\r\nmodule load apps\/gcc\/vcftools\/0.1.14-zlib1.2.8\r\n\r\nmodule load apps\/gcc\/vcftools\/0.1.14\r\n\r\nOR\r\n\r\nmodule load apps\/gcc\/vcftools\/0.1.11\r\n<\/pre>\n<h2>Running the application<\/h2>\n<p>Please do not run VCFtools on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n<h3>Serial batch job submission<\/h3>\n<p>Coming soon.<\/p>\n<h3>Parallel batch job submission<\/h3>\n<p>Coming soon.<\/p>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"http:\/\/vcftools.sourceforge.net\">VCFtools website<\/a><\/li>\n<\/ul>\n<h2>Updates<\/h2>\n","protected":false},"excerpt":{"rendered":"<p>Overview VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide methods for working with VCF files: validating, merging, comparing and calculate some basic population genetic statistics. Version 0.1.14 is installed on the CSF. It was compiled with gcc 4.9.0. There is a version 0.1.14 which uses zlib 1.2.8 which may give better performance. Version 0.1.11 is also.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/vcftools\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":31,"menu_order":0,"comment_status":"open","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-1240","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/1240","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\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/comments?post=1240"}],"version-history":[{"count":7,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/1240\/revisions"}],"predecessor-version":[{"id":3544,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/1240\/revisions\/3544"}],"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=1240"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}