{"id":457,"date":"2013-04-26T15:03:42","date_gmt":"2013-04-26T15:03:42","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=457"},"modified":"2016-08-01T14:14:49","modified_gmt":"2016-08-01T14:14:49","slug":"samtools","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/samtools\/","title":{"rendered":"SAMtools"},"content":{"rendered":"<h2>Overview<\/h2>\n<p>SAM (Sequence Alignment\/Map) format is a generic format for storing large nucleotide sequence alignments. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.<\/p>\n<p>Version 1.3.1 is available on the CSF (it was compiled with gcc 4.7.0) and includes tabix.<br \/>\nVersion 0.1.18 is available on the CSF (it was compiled with gcc 4.4.6)<\/p>\n<h2>Restrictions on use<\/h2>\n<p>SAMtools is open source, under the MIT License, and available to all users.<\/p>\n<h2>Set up procedure<\/h2>\n<p>To access SAMtools please load the modulefile:<\/p>\n<pre class=\"in1\">module load apps\/gcc\/samtools\/1.3.1 <\/pre>\n<p>or<\/p>\n<pre class=\"in1\">module load apps\/gcc\/samtools\/0.1.18 <\/pre>\n<h2>Running the application<\/h2>\n<h3>Serial batch job submission<\/h3>\n<p>Coming soon &#8230;<\/p>\n<h3>Parallel batch job submission<\/h3>\n<p>Coming soon &#8230;<\/p>\n<h2>Further info<\/h2>\n<ul>\n<li>The <a href=\"http:\/\/www.htslib.org\/\">SAMtools website<\/a> has documentation and an FAQ.<\/li>\n<li>The <a href=\"http:\/\/samtools.sourceforge.net\/\">old SAMtools website<\/a> may contain information relevant to releases prior to 0.1.x.\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Overview SAM (Sequence Alignment\/Map) format is a generic format for storing large nucleotide sequence alignments. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Version 1.3.1 is available on the CSF (it was compiled with gcc 4.7.0) and includes tabix. Version 0.1.18 is available on the CSF (it was compiled with gcc 4.4.6) Restrictions on use SAMtools is open source, under.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/samtools\/\">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-457","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/457","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=457"}],"version-history":[{"count":5,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/457\/revisions"}],"predecessor-version":[{"id":3283,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/457\/revisions\/3283"}],"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=457"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}