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Joint calling cases/controls
I have aprox.100cases and 100controls (WES). Would you rather run joint calling (according to GATK best practises) on cases and controls separately or jointly call cases and controls?
If I have a rare variant that is present in only few cases and not present in controls, will the variant be rescue in jointly called cases only? Will it also be rescue in cases and controls called together ?
What are the caveats of both methods (jointly/separately).