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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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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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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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samtools view -b yeast_pairedend.sort.sam -o yeast_pairedend.bam |
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