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VariantRecalibrator accepts only one VCF file?

tommycarstensentommycarstensen United KingdomMember ✭✭✭

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!

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