Samtools

Introduction

Samtools is a set of utilities for the Sequence Alignment/Map (SAM) format.

For more information, please check:
Docker hub: https://hub.docker.com/r/staphb/samtools
Home page: https://github.com/samtools/samtools

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

1.9, 1.15, 1.16, 1.17

BELL

1.9, 1.15, 1.16, 1.17, 1.22.1

GAUTSCHI

1.9, 1.15, 1.16, 1.17, 1.22.1

NEGISHI

1.9, 1.15, 1.16, 1.17, 1.22.1

SCHOLAR

1.9, 1.15, 1.16, 1.17

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

Module

You can load the modules by:

module load biocontainers
module load samtools

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run samtools on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition 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 --force purge
module biocontainers samtools

# Your samtools workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#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 --force purge
module biocontainers samtools

# Your samtools workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#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 --force purge
module biocontainers samtools

# Your samtools workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#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 --force purge
module biocontainers samtools

# Your samtools workflow...

#!/bin/bash
#SBATCH -A queue     # Queue 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 --force purge
module biocontainers samtools

# Your samtools workflow...