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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?