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This section contains articles related to developing for the GATK. Topics covered include how to write new walkers and Queue scripts, as well as some deeper GATK engine information that is relevant for developers.

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This section contains tutorials that will teach you step-by-step how to use GATK tools and how to solve common problems.
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The documentation articles in this section cover:

  • Methods using individual tools: articles providing recommendations on how to apply the tools on your data to answer specific questions or achieve certain data transformations. These articles are meant to complement the Technical Documentation available for each tool.
  • Workflows using several tools: articles describing how to chain several tools together appropriately into multi-step analyses and pipelines.
  • Computational methods: these articles describe how the GATK tools work and how to use them efficiently.

Please note that while many of the articles contain command lines and argument values, these are given as examples only and may not be the most appropriate for your dataset. It is your responsibility to ascertain that the parameters you use for analysis make sense considering your experimental design and materials.

In addition, certain examples, argument names, usages and values may become obsolete over time. We try to update the documentation regularly but some articles may fall through the net. This occasionally leads to apparent contradictions between articles in this section and the Technical Documentation that is available for each tool. When in doubt, keep in mind that the Technical Documentation is updated more frequently and always trumps other documentation sources.

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This section lists (and answers!) frequently asked questions.

These documentation articles cover specific points of clarification about the following:

  • details of how the GATK tools work and how they should be applied to datasets
  • questions that are related to NGS formats and concepts but are not specific to the GATK
  • questions about the community forum, documentation website and user support system
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Information about forum features and events impacting support will be announced here. Only forum administrators and moderators are able to post new discussions. Please feel free to comment on existing discussions.
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