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We have used several alignment methods that all generate results in the form of the near-universal SAM/BAM file format.  The SAMtools program is an a ubiquitously used set of tools that allow a user to manipulate SAM/BAM files in many different ways, ranging from simple tasks (like SAM/BAM interconversion) to more complex functions (like removal of PCR duplicates).  It is available in the TACC module system in the typical fashion.

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Code Block
Program: samtools (Tools for alignments in the SAM format)
Version: 1.2 (using htslib 1.2.1)
Usage:   samtools <command> [options]
Commands:
  -- indexing
         faidx       index/extract FASTA
         index       index alignment
  -- editing
         calmd       recalculate MD/NM tags and '=' bases
         fixmate     fix mate information
         reheader    replace BAM header
         rmdup       remove PCR duplicates
         targetcut   cut fosmid regions (for fosmid pool only)
  -- file operations
         bamshuf     shuffle and group alignments by name
         cat         concatenate BAMs
         merge       merge sorted alignments
         mpileup     multi-way pileup
         sort        sort alignment file
         split       splits a file by read group
         bam2fq      converts a BAM to a FASTQ
  -- stats
         bedcov      read depth per BED region
         depth       compute the depth
         flagstat    simple stats
         idxstats    BAM index stats
         phase       phase heterozygotes
         stats       generate stats (former bamcheck)
  -- viewing
         flags       explain BAM flags
         tview       text alignment viewer
         view        SAM<->BAM<->CRAM conversion

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Tip
titleSAMtools version differences

The most recent edition of SAMtools is 1.2, which has some important differences from the last version, 0.1.19.  Everything for this section is the same between the two versions, but if you see code from other sources using samtools, the version difference may be important.

Samtools view

The utility samtools view provides a way of converting SAM (text format) files to BAM (binary, compressed) files directly. It also provides many, many other functions which we will discuss lster. To get a preview, execute samtools view without any other arguments. You should see:

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Code Block
languagebash
samtools view -b yeast_pairedend.sort.sam -o yeast_pairedend.bam

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