Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Where are the links for the accepted variant file formats?
I am trying to format files for input into the BaseRecalibrator and VariantsToVcf tools. Many of the links for file formats listed on the 'variant' option do not work (http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_VariantsToVCF.html#--variant). I get the following message:
The requested URL /gatk/gatkdocs/org_broad_tribble_bed_BEDCodec.html was not found on this server.**
Do you know what the problem is?