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Better Search tools and I like to see more examples.

HideoHideo Member
edited August 2012 in Ask the GATK team

I posted my displeasure about the new web interface in twitter and MP suggested I should whine about it in this forum... So, I am very excited about a new GATK version and wanted know about new functions. But at the home page, I did not see a search function, which should be there. If I google something about GATK, currently google points me to a defunct page, which then points me to the current home page.

At the "community", I can find a search function but it often points to discussions. Once I know about GATK functions, it is easer to navigate but it took me quite a while to find out how to detect indels with GATK, even though it is simple once I know where to find. For example, when I type "Detecting Indel", I had hard time to find a GATK command for it.

I think GATK has one of the best supporting information and discussion on the web among sequence tools, which is why I started using it instead of Freebayes and etc. I know the web is still transient, but the web structure can be better.

I would be happy if it offers search engines:
1. for purely functional basic information
2. for medium level users
3. for advanced users
4. discussions

I would like to see
5. user provided examples: Officially GATK people are not responsible of their validity but it is good to know specific parameter values people are using since these parameters can be quite different for different organisms, as more people are working on very unconventional organisms whose genome behaviour does not follow those of model organisms.



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Thanks for your feedback, Hideo.

    We are aware that the current search function is inadequate, and we are currently testing some alternative solutions. We hope to be able to resolve this on the website very soon. We may not be able to implement the level filtering system you suggest right away, but it's an interesting idea that we will certainly explore.

    We're also working on providing more examples and tutorials to illustrate recommended tool usage.

    And we would be happy to host user-provided examples as well! However this needs to be more of a grass-roots effort, so please feel free to submit examples from your own experience, and encourage colleagues to do the same. This would be appropriate to post in the "Ask the community" section of the forum.

    We apologize for the inconveniences that the website's "growing pains" are causing you -- we are working hard to resolve them asap. Thanks for taking the time to let us know what is causing you the most trouble.

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