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HaplotypeCaller vs GCF->GenotypeGVCFs workflow for small WES cohorts
For small WES (whole exome) cohorts such as trios, is it better to:
a) Do HaplotypeCaller jointly on the trio exome BAM files
b) Do HaplotypeCaller on each individual WES BAM file individually in GVCF mode, followed by CombineGVCFs, followed by GenotypeGVCFs?
Or... do (a) and (b) produce equivalent results?
I'm assuming that the computational resources difference between (a) and (b) is not significant enough to warrant deciding on anything other than purely best accuracy (i.e. sensitivity and specificity).