samtools
Link to section 'Description' of 'samtools' Description
SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format
Link to section 'Versions' of 'samtools' Versions
- Anvil: 1.12
Link to section 'Commands' of 'samtools' Commands
- ace2sam
- blast2sam.pl
- bowtie2sam.pl
- export2sam.pl
- fasta-sanitize.pl
- interpolate_sam.pl
- maq2sam-long
- maq2sam-short
- md5fa
- md5sum-lite
- novo2sam.pl
- plot-ampliconstats
- plot-bamstats
- psl2sam.pl
- sam2vcf.pl
- samtools
- samtools.pl
- seq_cache_populate.pl
- soap2sam.pl
- wgsim
- wgsim_eval.pl
- zoom2sam.pl
Link to section 'Module' of 'samtools' Module
You can load the modules by:
module load samtools
Link to section 'Example job' of 'samtools' Example job
To run Samtools on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=samtools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module load samtools
samtools sort my.sam > my_sorted.bam
samtools index my_sorted.bam