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This page shows you how to run GATK4 using our recently installed Singularity GATK4 container. The runAsPipeline script, accessible through the rcbio/1.0 module, converts the bash script into a pipeline that easily submits jobs to the Slurm scheduler for you.

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The workflows are downloaded from: https://github.com/gatk-workflows/gatk4-rnaseq-germline-snps-indels and modified to work on O2 slurm cluster.

Notice the original workflow uses reference and annotation files listed in this file: 

https://github.com/gatk-workflows/gatk4-rnaseq-germline-snps-indels/blob/master/gatk4-rna-germline-variant-calling.inputs.json 

We download the genome reference and all annotation files from: 

https://console.cloud.google.com/storage/browser/genomics-public-data/references/Homo_sapiens_assembly19_1000genomes_decoy/ except for the gtf file, which is downloaded from here: https://console.cloud.google.com/storage/browser/gatk-test-data/intervals?project=broad-dsde-outreach

We then modified the json file to this one: 

/n/shared_db/singularity/hmsrc-gatk/scripts/gatk4-rna-germline-variant-calling.inputs.template.json

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# This will setup the path and environmental variables for the pipeline
module load gcc/6.2.0 python/2.7.12 java/jdk-1.8u112 star/2.5.4a rcbio/1.3.3
export PATH=/n/shared_db/singularity/hmsrc-gatk/bin:/home/ld32/rcbioDev/bin:$PATH

# setup database. Only need run this once. It will setup database in home, so make sure you have at least 5G free space at home.
setupDB.sh

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