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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 of samtools:

$ module avail samtools

Load a particular version of samtools:

$ module load samtools/1.5


Notes from the sysadmin during installation:

$ cd /tmp
$ wget
$ tar xf samtools-1.5.tar.bz2
$ cd samtools-1.5
$ scl enable devtoolset-4 bash
$ sudo mkdir /export/apps/samtools/1.5
$ sudo chown aorth /export/apps/samtools/1.5
$ ./configure --enable-plugins --enable-libcurl --without-curses --prefix=/export/apps/samtools/1.5
$ make all all-htslib
$ make install install-htslib
$ sudo chown -R root:root /export/apps/samtools/1.5
samtools-software.txt · Last modified: 2017/06/30 18:02 by aorth