Page Comparison

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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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From a Mac Terminal, use the ssh command, inserting your eCommons HMS ID instead of user123:

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  # start screen session. For detail: https://wiki.rc.hms.harvard.edu/pages/viewpage.action?pageId=20676715

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