Not sure whether this is the right place to put this, or even the right forum to ask but I was wondering whether it was possible to add custom annotations to the FORMAT field rather than the INFO field? If not GATK, do any third party programs able to handle such a request?
Thanks! Appreciate any help.
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: **Not Found
The requested URL /gatk/gatkdocs/org_broad_tribble_bed_BEDCodec.html was not found on this server.**
Do you know what the problem is?