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The SAM format is a standard format for storing large nucleotide sequence alignments. The BAM format is just the binary form from SAM. SAMtools (http://samtools.sourceforge.net/) 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:

General SAMtools Usage
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:

General SAMtools COMMAND Options
[<username>@login.tusker~]$ samtools COMMAND

or check the SAMtools manual: http://samtools.sourceforge.net/samtools.shtml.

The page Running SAMtools Commands shows how to run SAMtools on HCC.

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