Difference between revisions of "Samtools"
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Moskalenko (talk | contribs) m (Text replace - "Usage policy" to "Usage Policy") |
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{{#if: {{#var: pbs}}|==PBS Script Examples== | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
| − | {{#if: {{#var: policy}}|==Usage | + | {{#if: {{#var: policy}}|==Usage Policy== |
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)|}} | ||
{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
Revision as of 16:33, 10 August 2012
Description
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.
Note: The Samtools 0.1.18 install includes the tabix and bgzip binaries from the Tabix-0.2.6 software.
Execution Environment and 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