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Comparing output VCF quality with and without Scatter Gather
I would like to know if the VCF output and its quality will remain the same with and without Scatter Gather.
(a) Running HaplotypCaller one regular mode
(b) HaplotypCaller with Scatter gather (scattering by sample)
(c) HaplotypCaller with Scatter gather (scattering by locus)
(d) HaplotypCaller with Scatter gather (scattering by chromosome)
Has anyone done this comparison ?