Congrats on the version 4 release.
Now the page are updated to 4 but I'm currently still working on 3.8, is there a link I can find the old best practice documents?
The old documentation articles are still available; you can switch to them using the orange dropdown menu that switches between GATK4 and GATK3, which gets you eg https://software.broadinstitute.org/gatk/documentation/topic?name=methods&v=3
where the &v=3 part of the URL is what switches versions.
However the Best Practices webpages themselves which collated all the articles are no longer available; it was too complicated to keep them around too -- sorry!
However the generalities of the germline Best Practices are still essentially the same, it's only the argument names that changed. Is there anything specific you need to look up that you're not finding?
is possible to have the "VQSR Best Practice" code, all 4 steps (GenomeAnalysisTK-3.8-1-0-gf15c1c3ef)?
Sorry, I am not sure what you mean?
I was using VQSR of GATK3 and I wanted to check my steps with the BEST PRACTICE of GATK3.
Now I shifted at VQSR of GATK4 and I don't need it any more.
Thank you very much,