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.
From GATK 2.7 to 3.2, we noticed that the FILTER field changed using VariantRecalibration.
Previously, we had the filter names in regards to the model build by the VariantsRacalibration. Now it's either PASS or LOW_VSQLOD
Is there a way to have the ApplyRecalibration walker assign the tranche name as filter, ie
instead of only LOW_VSQLOD ?