Difference between revisions of "Samtools"
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(Created page with "Installed in /apps/samtools/0.1.16") |
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| − | + | __NOTOC__ | |
| + | __NOEDITSECTION__ | ||
| + | [[Category:Software]][[Category:Bioinformatics]][[Category:NGS]] | ||
| + | <!-- ######## Template Configuration ######## --> | ||
| + | <!--Edit definitions of the variables used in template calls | ||
| + | Required variables: | ||
| + | app - lowercase name of the application e.g. "amber" | ||
| + | url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/" | ||
| + | Optional variables: | ||
| + | INTEL - Version of the Intel Compiler e.g. "11.1" | ||
| + | MPI - MPI Implementation and version e.g. "openmpi/1.3.4" | ||
| + | --> | ||
| + | {| | ||
| + | <!--Main settings - REQUIRED--> | ||
| + | |{{#vardefine:app|samtools}} | ||
| + | |{{#vardefine:url|http://samtools.sourceforge.net/}} | ||
| + | <!--Compiler and MPI settings - OPTIONAL --> | ||
| + | |{{#vardefine:intel|}} <!-- E.g. "11.1" --> | ||
| + | |{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" --> | ||
| + | <!--Choose sections to enable - OPTIONAL--> | ||
| + | |{{#vardefine:mod|1}} <!--Present instructions for running the software with modules --> | ||
| + | |{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | ||
| + | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | ||
| + | |{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | ||
| + | |{{#vardefine:policy|}} <!--Enable policy section --> | ||
| + | |{{#vardefine:testing|}} <!--Enable performance testing/profiling section --> | ||
| + | |{{#vardefine:faq|}} <!--Enable FAQ section --> | ||
| + | |{{#vardefine:citation|}} <!--Enable Reference/Citation section --> | ||
| + | |} | ||
| + | <!-- ######## Template Body ######## --> | ||
| + | <!--Description--> | ||
| + | {{#if: {{#var: url}}| | ||
| + | {{App_Description|app={{#var:app}}|url={{#var:url}}}}|}} | ||
| + | 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. | ||
| + | <!--Location--> | ||
| + | {{App_Location|app={{#var:app}}|{{#var:ver}}}} | ||
| + | ==Available versions== | ||
| + | * 0.1.16 | ||
| + | * 0.1.18 (default) | ||
| + | <!-- --> | ||
| + | {{#if: {{#var: mod}}|==Running the application using modules== | ||
| + | {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | ||
| + | * HPC_SAMTOOLS_BIN - executable directory | ||
| + | {{#if: {{#var: exe}}|==How To Run== | ||
| + | See "man samtools" for a command line version of the samtools help. | ||
| + | |}} | ||
| + | {{#if: {{#var: conf}}|==Configuration== | ||
| + | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | ||
| + | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
| + | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
| + | {{#if: {{#var: policy}}|==Usage policy== | ||
| + | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | ||
| + | {{#if: {{#var: testing}}|==Performance== | ||
| + | WRITE PERFORMANCE TESTING RESULTS HERE|}} | ||
| + | {{#if: {{#var: faq}}|==FAQ== | ||
| + | *'''Q:''' **'''A:'''|}} | ||
| + | {{#if: {{#var: citation}}|==Citation== | ||
| + | If you publish research that uses {{{app}}} you have to cite it as follows: | ||
| + | WRITE CITATION HERE | ||
| + | |}} | ||
Revision as of 19:12, 7 February 2012
Description
{{{name}}} website
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.
Template:App Location
Available versions
- 0.1.16
- 0.1.18 (default)
Running the application using modules
To use samtools with the environment modules system at HPC the following commands are available:
Get module information for samtools:
$module spider samtools
Load the default application module:
$module load samtools
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_SAMTOOLS_DIR - directory where samtools is located.
- HPC_SAMTOOLS_BIN - executable directory