Difference between revisions of "Samtools"
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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. | 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. | ||
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'''Note:''' The Samtools 0.1.18 install includes the tabix and bgzip binaries from the Tabix-0.2.6 software. | '''Note:''' The Samtools 0.1.18 install includes the tabix and bgzip binaries from the Tabix-0.2.6 software. | ||
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{{#if: {{#var: mod}}|==Execution Environment and Modules== | {{#if: {{#var: mod}}|==Execution Environment and Modules== | ||
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | {{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}} | ||
Revision as of 02:51, 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