Can you please provide
a) GATK version used
b) Exact GATK commands used
c) The entire error log if applicable.
I am trying to do joint calling on multiple samples from this workflow:
This document reads like you need to aggregate individual gvcfs to one file to run GenotypeGVCF. This takes a very long time with hundreds of samples, even when splitting by chromosome.
This post actually seems counter and suggests you can run GenotypeGVCF on multiple individual samples:
If I run GenotypeGVCF on unmerged GVCF (one for each sample) do I still get the benefits of "joint calling"?
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