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.
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 !