SAMtools
The SAM format is a standard format for storing large nucleotide sequence alignments. The BAM format is just the binary form from SAM. SAMtools is a toolkit for manipulating alignments in SAM/BAM format, including sorting, merging, indexing and generating alignments in a per-position format.
The basic usage of SAMtools is:
$ samtools COMMAND [options]
where
COMMAND is one of the following SAMtools commands
:
- view: SAM/BAM and BAM/SAM 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
- 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
- phase: phase heterozygotes
- bamshuf: shuffle and group alignments by name
For detailed description and more information on a specific command, just type:
or check the
SAMtools manual.
The page Running SAMtools Commands shows how to run SAMtools on HCC.