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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-data-processing and https://github.com/gatk-workflows/gatk4-somatic-snvs-indels
Jumpstart
Here are the commands to test out the workflow using example data. The whole run needs a few hours if the cluster is not busy.
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ssh user123@o2.hms.harvard.edu # set up screen software: https://wiki.rc.hms.harvard.edu/pages/viewpage.action?pageId=20676715 cp /n/shared_db/misc/rcbio/data/screenrc.template.txt ~/.screenrc screen srun --pty -p interactive -t 0-12:0:0 --mem 16000MB -n 2 /bin/bash mkdir -p /n/scratch3scratch/users/${USER:0:1}/$USER/testGATK4 cd /n/scratch3scratch/users/${USER:0:1}/$USER/testGATK4 module load gcc/6.2.0 python/2.7.12 rcbio/1.3.3 export PATH=/n/shared_db/singularity/hmsrc-gatk/bin:/opt/singularity/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 cp /n/shared_db/singularity/hmsrc-gatk/scripts/* . buildSampleFoldersFromSampleSheet.py sampleSheet.xlsx runAsPipeline fastqToBam.sh "sbatch -p short --mem 4G -t 1:0:0 -n 1" noTmp run 2>&1 | tee output.log # check email or use this command to see the workflow progress squeue -u $USER -o "%.18i %.9P %.28j %.8u %.8T %.10M %.9l %.6D %R %S" # After all jobs finish run, run this command to start database, and keep it running in background runDB.sh & java -XX:+UseSerialGC -Dconfig.file=your.conf -jar /n/shared_db/singularity/hmsrc-gatk/cromwell-43.jar run processing-for-variant-discovery-gatk4.wdl -i unmappedBams/group1/in.json 2>&1 | tee -a group1.log java -XX:+UseSerialGC -Dconfig.file=your.conf -jar /n/shared_db/singularity/hmsrc-gatk/cromwell-43.jar run processing-for-variant-discovery-gatk4.wdl -i unmappedBams/group2/in.json 2>&1 | tee -a group2.log setupJson.sh java -XX:+UseSerialGC -Dconfig.file=your.conf -jar /n/shared_db/singularity/hmsrc-gatk/cromwell-43.jar run mutect2.wdl -i unmappedBams/exon.json && findVCF.sh # Stop database killall runDB.sh |
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srun --pty -p interactive -t 0-12:0:0 --mem 16000MB -n 2 /bin/bash mkdir -p /n/scratch3scratch/users/${USER:0:1}/$USER/testGATK4 cd /n/scratch3scratch/users/${USER:0:1}/$USER/testGATK4 |
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