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Any way to download hellbender-all-1.0.jar?

daxuedaxue Member
edited July 2017 in Ask the FireCloud Team

Hi,

I'm trying to reproduce some Firecloud best practice workflows locally. However, some files used in the workflows could not be downloaded. For example, /usr/local/bin/hellbender-all-1.0.jar was used in Mutect best practice workflow. As the file does not appear in the list of downloadable Input files and the path of this file is not /cromwell_root/firecloud-tcga-open-access based (so could not get gs:// style address for gsutil), I couldn't find a way to download it yet. As the workflow could access this file, I think there might be some way to download it as well.

Also, "hellbender" is the code name of GATK 4. This file looks like a certain version of GATK 4. However, all versions of publicly available GATK 4 do not have the command "CreateEvenIntervals", which is used in the Mutect workflow. A command looking close to "CreateEvenIntervals" is "SplitIntervals". However, "SplitIntervals" seems only work for BAM/SAM/CRAM files, while "CreateEvenIntervals" works for interval files.

Any feedback are highly appreciated. Thank you.

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