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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/1.8


Notes from the sysadmin during installation:

$ cd /tmp
$ wget
$ tar xf samtools-1.8.tar.bz2 
$ cd samtools-1.8
$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/samtools/1.8 --with-htslib=/export/apps/htslib/1.8
$ make
$ sudo mkdir /export/apps/samtools/1.8
$ sudo chown aorth:aorth /export/apps/samtools/1.8
$ make install
$ sudo chown -R root:root /export/apps/samtools/1.8

This links against a system-wide version of htslib/1.8.

samtools-software.txt · Last modified: 2018/06/01 22:31 by aorth