Skip to content

samtools: SAM (Sequence/Alignment Mapping) Tools

Overview of package

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

General Usage

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 by cluster

This section lists the available versions of the package samtoolson the UMD HPC clusters.

Versions available on the Zaratan cluster

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