Samtools

Description

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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. Template:App Location

Available versions

• 0.1.16
• 0.1.18 (default)

Note: The Samtools 0.1.18 install includes the tabix and bgzip binaries from the Tabix-0.2.6 software.

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