Samtools 2.2.1

Samtools is a suite of programs for interacting with high-throughput sequencing data. Used for Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format

Usage

Example script : test-samtools.sh

#!/bin/bash

#SBATCH -J samtools-test
#SBATCH -e samtools-test%j.err
#SBATCH -o samtools-test%j.msg
#SBATCH -p thin # queue (partition)

# load samtools
module load samtools/1.21

# list samtools root folder
ls -al $SAMTOOLS_ROOT

# list samtools binaries
ls -al $SAMTOOLS_ROOT/compiled/bin/

samtools --help

echo "DONE!"

Submit with :

sbatch --account=your_project_ID test-samtools.sh

More info :

• https://www.htslib.org/