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calling variants in multiple samples
i have sequenced two exomes from two affected individuals from the same family.
i have called their variants with the recommended UnifiedGenotyper protocol for each sample individually (was done a year and half ago..), and then did theintersection to find teh shared ones.
i was wondering, if you recommend calling them at one step, togther? is there any added value for doing so (in term of reducing false positives, accuracy etc..).