The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
Sorry I'm not clear on one point:
Say I want to run VQSR on a set of 30 samples (exomes).
Do I need to run genotypeGVCFs on all 30 GVCF files, and then feed the single joint VCF
output into variantrecalibrator,
do I need to feed the 30 individual VCF files into variantrecalibrator?