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Better Search tools and I like to see more examples.
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
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.