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I'm trying to run the HaplotypeCaller in GATK2.5. I hope to get the confident reference calls as UnifiedGenotyper outputs, so I set the option "-out_mode EMIT_ALL_CONFIDENT_SITES". However, I notice the total number of reference calls HaplotypeCaller makes is really small. I'm wondering could you provide any information on how HaplotyperCaller decides where to/not to output the reference calls please?