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Picard Leaps Into the Future!

deklingdekling Broad InstituteMember

Greetings fellow citizens of the Galactic Commonwealth. We the GATK Support Team welcome you once again to our understated, yet exceptionally informative blog.

As you may or may not know, the GATK and Picard toolkits are on converging arcs, and will eventually be merged into the unified super-beefed up toolkit that will be GATK 4. In preparation for that bright future, we have been fielding Picard usage-related questions in the GATK forum, and we have now officially taken over stewardship of the Picard documentation.

As it is so often said, with great power comes great responsibility. Our mission is to help make the user experience, as painless as humanly possible. “How does the support team carry out this challenging yet critically important task”, you ask?

Well, we've just completed our first big push on two fronts. In terms of content, we added a lot of new information to the Picard tool documentation, to provide more detail on what the tools do and how to use them optimally. Most recently, we've also been making some substantial changes to the organization of the content, as well as tweaking the general look and feel of the website.


Here are a few highlights:

  • We rewrote the Quick Start instructions to focus on those of you who just want to download the program and get to work analyzing your data. These streamlined instructions now walk you through the process of downloading the pre-compiled Picard executable, testing that it runs on your system, and pointing you to relevant resources for getting started with using the tools.

  • For those of you who enjoy tinkering with source code, you'll find all necessary (up-to-date!) instructions for building from source and more in the README.md doc on GitHub.

  • The FAQ page has been updated! Notice that dead links have been resurrected and many new links have been added.

  • The Tool Documentation page now includes a detailed overview of the command line syntax, a list of standard options, and an updated list of required and optional arguments for each tool. Moreover, most of the tool docs now include handy command line examples as well as recommendations regarding important yet optional arguments.

  • On the Metrics Definitions page, you will find that additional details have been added to facilitate data analysis.

  • We also refurbished the page that explains SAM flags, which had inexplicably been left without any styling all these years.

But wait! We're not done! We strive to do everything possible to enhance usability and functionality of our tools. If something does not seem right, post a note in the Forum and we will address your concerns as quickly as possible.

Until next time, [lift]over and out[put]!

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