SAMtools¶
SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
SAMtools is available as a module on Apocrita.
Usage¶
To run the default installed version of SAMtools, simply load the samtools
module:
module load samtools
then run one of the SAMtools commands such as:
samtools view -b -S -o genome_reads_aligned.bam genome_reads_aligned.sam
Core Usage
To ensure that SAMtools uses the correct number of cores, the
-@ ${NSLOTS} option should be used on commands that support it.
Deprecated feature
Note that using samtools mpileup to generate BCF or VCF files has been
removed. To output these formats, please use bcftools mpileup instead.
Example job¶
Serial job¶
Here is an example job running on 4 cores and 8GB of memory:
#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 4
#$ -l h_rt=1:0:0
#$ -l h_vmem=2G
module load samtools bcftools
samtools view -@ ${NSLOTS} -b -S -o genome_reads_aligned.bam \
genome_reads_aligned.sam
samtools sort -@ ${NSLOTS} genome_reads_aligned.bam \
> genome_reads_aligned.sorted.bam
samtools index genome_reads_aligned.sorted.bam