Gatk4

Introduction

GATK (Genome Analysis Toolkit) is a collection of command-line tools for analyzing high-throughput sequencing data with a primary focus on variant discovery.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/gatk4
Home page: https://www.broadinstitute.org/gatk/

Note

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

Versions

Cluster	Version(s)
ANVIL	4.2.0, 4.2.5.0, 4.2.6.1, 4.3.0.0, 4.6.0.0
BELL	4.2.0, 4.2.5.0, 4.2.6.1, 4.3.0.0, 4.6.0.0
GAUTSCHI	4.2.0, 4.2.5.0, 4.2.6.1, 4.3.0.0, 4.6.0.0
NEGISHI	4.2.0, 4.2.5.0, 4.2.6.1, 4.3.0.0, 4.6.0.0
SCHOLAR	4.2.0, 4.2.5.0, 4.2.6.1, 4.3.0.0

Commands

gatk

Module

You can load the modules by:

module load biocontainers
module load gatk4

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 gatk4 on our clusters:

Anvil

#!/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=gatk4
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers gatk4

# Your gatk4 workflow...

Bell, Gautschi, or Negishi

#!/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=gatk4
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers gatk4

# Your gatk4 workflow...

Gautschi-AI

#!/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=gatk4
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers gatk4

# Your gatk4 workflow...

Gilbreth

#!/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=gatk4
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers gatk4

# Your gatk4 workflow...

Scholar

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=gatk4
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers gatk4

# Your gatk4 workflow...