Container for the GATK

Tools included

1. SamTools
2. BWA
3. Datamash
4. GATK
5. Picard Tools
6. BioAWK
7. BedTools

Please be sure to cite all the programs if you use this container.

Singularity

to pull the image

singularity pull --name gatk.sif shub://aseetharam/gatk:latest

to use the image

singularity exec gatk.sif samtools
singularity exec gatk.sif bwa
singularity exec gatk.sif datamash
singularity exec gatk.sif java -jar /gatk/gatk-package-4.1.8.1-local.jar
singularity exec gatk.sif java -jar /picard/picard.jar
singularity exec gatk.sif bioawk
singularity exec gatk.sif bedtools