HPC:samtools
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samtools
samtools versions 0.1.18 and 0.1.19 are installed on all HPC nodes.
samtools v0.1.18 is the system default :
[asrini@node061 ~]$ which samtools
/usr/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
If you need to use samtools v0.1.19, use the environment module:
[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
