Container for the GATK

Installed software:

1. apt pacakges list
2. python packages list
3. r pacakges list
4. conda packages list

Please be sure to cite all the programs (not this repository) if you use this container.

Singularity

to pull the image

# from Docker hub
singularity pull --name gatk_4.4.0.sif docker://arnstrm2/gatk:4.4.0
# from GitHub
singularity pull docker://ghcr.io/aseetharam/gatk:master

Docker

to pull the image

# from Docker hub
docker pull arnstrm2/gatk:4.4.0
# from GitHub
docker pull ghcr.io/aseetharam/gatk:master

Example usage

singularity exec gatk_4.4.0.sif samtools
singularity exec gatk_4.4.0.sif bwa
singularity exec gatk_4.4.0.sif bwa-mem2
singularity exec gatk_4.4.0.sif bioawk
singularity exec gatk_4.4.0.sif datamash
singularity exec gatk_4.4.0.sif vcftools
singularity exec gatk_4.4.0.sif bcftools
singularity exec gatk_4.4.0.sif bedtools
singularity exec gatk_4.4.0.sif STAR
singularity exec gatk_4.4.0.sif minimap2
singularity exec gatk_4.4.0.sif pbmm2
singularity exec gatk_4.4.0.sif freebayes
singularity exec gatk_4.4.0.sif java -jar /opt/snpEff/snpEff.jar
# running gatk tools
singularity exec gatk_4.4.0.sif gatk --spark-runner LOCAL CreateSequenceDictionary # or
singularity exec gatk_4.4.0.sif java -jar /gatk/gatk-package-4.4.0.0-local.jar CreateSequenceDictionary # or
singularity exec gatk_4.4.0.sif java -jar /gatk/gatk.jar CreateSequenceDictionary