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.
VariantRecalibrator accepts only one VCF file?
The documentation on VariantRecalibrator reads:
--variant -V  One or more VCF files containing variants
However, when I supply multiple VCF files I get this error message:
A USER ERROR has occurred: Invalid argument 'out_GenotypeGVCFs/2nd.vcf.gz'.
Previously one could do
--input vcfs.list. Now it seems the VCFs have to be merged prior to running VariantRecalibrator? Thanks!