Our expert says:
If the doctor can't with 100% certainty say that the person died of "natural causes", an autopsy must be done. For instance if a person has terminal cancer at home and then dies, the treating doctor would "expect" the person to die of the disease and will probably give a certificate stating the cause of death as natural, but if the person was fairly healthy and then suddenly dies, an autopsy is often requested if the doctor is not sure of the cause of death. In your dad's case, the doctor could probably not say exactly what caused your dad's death and therefor an autopsy was requested.
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