Difference between revisions of "HPC:samtools"
From HPC wiki
| Line 1: | Line 1: | ||
=== samtools === | === samtools === | ||
| − | samtools versions 0.1.18 | + | samtools versions 0.1.18, 0.1.19 and 1.1 are installed on all HPC nodes. |
| − | samtools v0.1.18 is | + | '''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 : | ||
<pre> | <pre> | ||
[asrini@node061 ~]$ which samtools | [asrini@node061 ~]$ which samtools | ||
| − | /usr/bin/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 | [asrini@node061 ~]$ samtools | ||
| Line 33: | Line 43: | ||
</pre> | </pre> | ||
| − | + | Other versions of SAMtools like v0.1.19 are also available as the environment modules: | |
<pre> | <pre> | ||
Revision as of 11:12, 16 July 2015
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
