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GATK Showcase in Terra

Check out these fully configured workspaces to test drive the Best Practices pipelines and workshop tutorials with zero installation required!

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1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. When reporting a problem, include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.

Did we ask for a bug report?

Then follow instructions in Article#1894.

Did we give you a GitHub issue to track?

For GitHub basics see Article#23405.

Formatting tip!

Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

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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.

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Archives for April 2016

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

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