Comment: What is GenotypeGVCFs?

the second article is about RNASeq..

> in which cases should i use one or another?

> > “However, that scaled very poorly with the number of samples, posing unacceptable limits on the size of the study cohorts that could be analyzed in that way. In addition, it was not possible to add samples incrementally to a study; all variant calling work had to be redone when new samples were introduced.”

in a nutshell, use GVCF when HaplotypeCaller becomes too slow (=too many samples).
I use GVCF when WGS+N_SAMPLES>20.

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