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.
Is there a way to limit the genotyping to those sites with FILTER=PASS?
With the genotyping discovery qscript, all the discovery sites were genotyped during the run instead of the much smaller set that have filter=PASS.
Instead of having all these sites genotyped, is there a option to specify that only sites with filter=PASS should be genotyped and output to the final vcf file. Or is there a reason these non PASS sites are included?