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!