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.
ProduceBeagleInput feature request
After UnifiedGenotyper --genotype_likelihoods_model BOTH I have this INDEL: 1 10146 . AC A 22089 .
After ApplyRecalibration --mode SNP I still have this INDEL, however it is not marked as PASSed: 1 10146 . AC A 22089 .
If I apply ProduceBeagleInput directly to the AR output, then that INDEL is included in the PBI output.
You were kind enough to disallow CombineVariants from setting a FILTER value of PASS (http://gatkforums.broadinstitute.org/discussion/2647/combinevariants-removefilter-feature-request). As a low priority, can you give the option to disallow PBI from using variants, which do not have a FILTER value of PASS (or whatever value decided by the user)?
Thank you for a good tool kit.