HPC:samtools

SAMtools

samtools versions 0.1.18, 0.1.19 and 1.1 are installed on all HPC nodes.

Note 1: The path "opt/software/samtools/current/samtools" no longer exists. This was a symbolic link to an older version of SAMtools which has now been removed. Using the environment modules for the desired version of SAMtools as described in this section, is the appropriate way to run SAMtools on the PMACS HPC.

Note 2: There are no default versions of SAMtools. All versions of SAMtools installed on the PMACS HPC systems are now made available as modules.

samtools v0.1.18 is available as a module :

[asrini@node061 ~]$ which samtools
/usr/bin/which: no samtools in (/usr/share/lsf/9.1/linux2.6-glibc2.3-x86_64/bin:/usr/share/lsf/9.1/linux2.6-glibc2.3-x86_64/etc:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/asrini/bin)

[asrini@node061 ~]$ module load samtools-0.1.18 

[asrini@node061 ~]$ which samtools
/opt/software/samtools/0.1.18/bin/samtools

[asrini@node061 ~]$ samtools

Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.18 (r982:295)

Usage:   samtools <command> [options]

Command: view        SAM<->BAM conversion
         sort        sort alignment file
         mpileup     multi-way pileup
         depth       compute the depth
         faidx       index/extract FASTA
         tview       text alignment viewer
         index       index alignment
         idxstats    BAM index stats (r595 or later)
         fixmate     fix mate information
         flagstat    simple stats
         calmd       recalculate MD/NM tags and '=' bases
         merge       merge sorted alignments
         rmdup       remove PCR duplicates
         reheader    replace BAM header
         cat         concatenate BAMs
         targetcut   cut fosmid regions (for fosmid pool only)
         phase       phase heterozygotes

Other versions of SAMtools like v0.1.19 are also available as the environment modules:

[asrini@node061 ~]$ module load samtools-0.1.19

[asrini@node061 ~]$ which samtools
/opt/software/samtools/samtools-0.1.19/samtools

[asrini@node061 ~]$ samtools

Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.19-44428cd

Usage:   samtools <command> [options]

Command: view        SAM<->BAM conversion
         sort        sort alignment file
         mpileup     multi-way pileup
         depth       compute the depth
         faidx       index/extract FASTA
         tview       text alignment viewer
         index       index alignment
         idxstats    BAM index stats (r595 or later)
         fixmate     fix mate information
         flagstat    simple stats
         calmd       recalculate MD/NM tags and '=' bases
         merge       merge sorted alignments
         rmdup       remove PCR duplicates
         reheader    replace BAM header
         cat         concatenate BAMs
         bedcov      read depth per BED region
         targetcut   cut fosmid regions (for fosmid pool only)
         phase       phase heterozygotes
         bamshuf     shuffle and group alignments by name

Other Pages

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• HPC FAQ
• Connecting to the PMACS cluster
• User Guide
• Available Software
• PMACS Archive System