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.
ApplyVQSR page example error
Thanks for the wonderful development of this tool.
When I tried out ApplyVQSR with GATK4, I was following the examples from https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_vqsr_ApplyVQSR.php,
and found the option
--ts_filter_level in the example not recognised by GATK. Further reading on the page suggested the option should really be
--ts_filter_level was a carry over from GATK 3.x. Can you please correct it?