Samtools

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Description

samtools 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. 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