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what is the best order to use HC, GenotypeVCFs, VariantRecalibrate and CombineVariants?
I have 2 DNAseq batches of samples (more batches are ongoing sequencing, i.e. cohort). I used HaplotypeCaller per sample and got 2 batches of gvcfs, one gvcf per sample. But I am not sure which of the following order is best: (CombineGVCFs per batch) -> GenotypeGVCFs (obtain a single vcf) -> VariantRecalibration, or GenotypeGVCFs per batch -> VariantRecalibration per batch -> CombineVariant (obtain a single vcf). What is the difference between these two orders? and which one is more suitable for my situation? Hoping for any suggestions. Thank you very much !