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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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