samtools: SAM (Sequence/Alignment Mapping) Tools

Contents

1. Overview of package
   1. General usage
2. Availability of package by cluster

Overview of package

General information about package

Package:	samtools
Description:	SAM (Sequence/Alignment Mapping) Tools
For more information:	http://www.htslib.org
Categories:	Genomics
License:	OpenSource (BSD, MIT)

General usage information

SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format

This module will add the samtools and related commands to your PATH.

In case you need to link against this library in your code, the following environmental variables have been defined:

• \$SAMTOOLS_ROOT has been set to the root of the samtools installation
• \$SAMTOOLS_LIBDIR points to the directory containing the libraries
• \$SAMTOOLS_INCDIR points to the directory containing the header files

You will probably wish to use these by adding the following flags to your compilation command (e.g. to CFLAGS in your Makefile):

• -I\$SAMTOOLS_INCDIR

and the following flags to your link command (e.g. LDFLAGS in your Makefile):

• -L\$SAMTOOLS_LIBDIR -Wl,-rpath,\$SAMTOOLS_LIBDIR

Available versions of the package samtools, by cluster

This section lists the available versions of the package samtoolson the different clusters.

Available versions of samtools on the Zaratab cluster

Available versions of samtools on the Zaratab cluster

Version	Module tags	CPU(s) optimized for	GPU ready?
1.14	samtools/1.14	zen2	Y
1.17	samtools/1.17	icelake, x86_64, zen2	Y
1.10	samtools/1.10	zen	Y

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