I'm looking to use GATK's independent variant calling + joint genotyping workflow on a large pedigree with 10 different families. Is there any difference between the two approaches below:
- Run pipeline for all samples simultaneously
- Run pipeline for each family separately
I ask this because if the result of genotyping one family does not affect the results for other families, I might as well run them in parallel.
What do you say?
EDIT: I'm closing this question because I was mistaken in my assumption that GATK uses pedigree information during variant calling (HaplotypeCaller) or genotyping (GenotypeGVCFs).