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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.

GATK Guide Book

The User Guide on line at this URL
http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_genotyper_UnifiedGenotyper.html
has this text
Example command for generating calls at all sites
...
-o my.vcf \
...
--out / -o ( VariantContextWriter with default value stdout )
File to which variants should be written. A raw, unfiltered, highly sensitive callset in VCF format.

In my hands -o my.vcf produces an error message, complaining that there is no --out
while --out my.vcf works without error

Any suggestions?

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