Tabix is a generic indexer for TAB-delimited genome position files. Also provided is bgzip which is a block compression\/decompression utility. Closely associated with SAMtools<\/a>.<\/p>\n Version 0.2.6 is installed on the iCSF. It was compiled with gcc 4.7.0.<\/p>\n Version 1.3.1 is available through SAMtools<\/a><\/p>\n The software is open source. All iCSF users may access it.<\/p>\n To access the software you must first load the modulefile:<\/p>\n Version 1.3.1 is available through SAMtools<\/a><\/p>\n It is possible to use tabix to download vcf files, or, more usefully, portions of large vcf files from remote repositories. You should use Notice that in the above command we pipe the downloaded data (which is plain text data) through the gzip command to produce a compressed file named To view the contents of the compressed file (without needing to first incompress it) use the following command to page through it:<\/p>\n None.<\/p>\n","protected":false},"excerpt":{"rendered":" Overview Tabix is a generic indexer for TAB-delimited genome position files. Also provided is bgzip which is a block compression\/decompression utility. Closely associated with SAMtools. Version 0.2.6 is installed on the iCSF. It was compiled with gcc 4.7.0. Version 1.3.1 is available through SAMtools Restrictions on use The software is open source. All iCSF users may access it. Set up procedure To access the software you must first load the modulefile: module load apps\/gcc\/tabix\/0.2.6 Version.. Read more »<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":43,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-131","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/131","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\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/comments?post=131"}],"version-history":[{"count":10,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/131\/revisions"}],"predecessor-version":[{"id":667,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/131\/revisions\/667"}],"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=131"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}Restrictions on use<\/h2>\n
Set up procedure<\/h2>\n
\r\nmodule load apps\/gcc\/tabix\/0.2.6\r\n<\/pre>\n
Running the application<\/h2>\n
http:\/\/<\/code> when specifying the remote repository address, not ftp:\/\/<\/code> so that tabix can download through the University proxy server (Incline does not have direct access to the outside world – off-campus servers). For example:<\/p>\n\r\ntabix -fh http:\/\/ftp.1000genomes.ebi.ac.uk\/somepath\/blah.genotypes.vcf.gz \\\r\n 1:14720000-15600000 | gzip -c > data.vcf.gz\r\n<\/pre>\n
data.vcf.gz<\/code>. Text data usually compresses well and so this method will save you a lot of disk space.<\/p>\n\r\nzless data.vcf.gz\r\n<\/pre>\n
Further info<\/h2>\n
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Updates<\/h2>\n