Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Involving the svtoolkit/cookbook/.../set_sv_params.sh

I am running through the cookbook example given found at: http://software.broadinstitute.org/software/genomestrip/cookbook-genotyping-novel-site-1000-genomes-phase-1

The set_sv_params.sh file needs to be altered to properly format where metadata is stored. I have input

SV_METADATA_DIR= ~/GenomeSTRiP/svtoolkit/

as is, I get the following error message:

You must specify SV metadata location in scripts/set_sv_params.sh as SV_METADATA_DIR=...

Any insight that can help me overcome this error message?



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