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


Show all available versions:

$ module avail samtools

Load one version into your environment and run it:

$ module load samtools/1.15.1
$ samtools


Notes from the sysadmin during installation:

$ cd /tmp
$ wget
$ tar xf samtools-1.15.1.tar.bz2
$ cd samtools-1.15.1
$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/samtools/1.15.1 --with-htslib=/export/apps/htslib/1.15.1
$ make
$ sudo mkdir -p /export/apps/samtools/1.15.1
$ sudo chown aorth /export/apps/samtools/1.15.1
$ make install
$ sudo chown -R root:root /export/apps/samtools/1.15.1

This links against htslib/1.15.1, which is installed as a module. As of 1.15.1 this was compiled on CentOS 8 Stream.

samtools-software.txt · Last modified: 2022/06/23 09:35 by aorth