A method of identifying a subchromosomal aberration in a fetal genome of a fetus by analyzing a biological sample from a female subject pregnant with the fetus, the biological sample including cell-free DNA molecules from the female subject and the fetus, the method comprising: for each of a plurality of DNA molecules in the biological sample: measuring a size of the DNA molecule; identifying a location of the DNA molecule in a reference genome; determining, by a computer system, a count classification of a type of aberration for a first subchromosomal region by: determining a first amount of DNA molecules located in the first subchromosomal region; determining a second amount of DNA molecules located in a second region; computing a count parameter from the first amount and the second amount; and comparing the count parameter to one or more count thresholds to determine the count classification of the type of aberration existing in the biological sample for the first subchromosomal region; determining, by the computer system, a size classification for the first subchromosomal region by: calculating a first statistical value of sizes of DNA molecules located in the first subchromosomal region; calculating a reference statistical value of sizes of DNA molecules located in a reference region; determining a separation value between the first statistical value and the reference statistical value; and comparing the separation value to one or more size thresholds to obtain the size classification; and determining whether the fetus has the aberration in the first subchromosomal region based on the size classification and the count classification. for each of a plurality of DNA molecules in the biological sample: measuring a size of the DNA molecule; identifying a location of the DNA molecule in a reference genome; measuring a size of the DNA molecule; identifying a location of the DNA molecule in a reference genome; determining, by a computer system, a count classification of a type of aberration for a first subchromosomal region by: determining a first amount of DNA molecules located in the first subchromosomal region; determining a second amount of DNA molecules located in a second region; computing a count parameter from the first amount and the second amount; and comparing the count parameter to one or more count thresholds to determine the count classification of the type of aberration existing in the biological sample for the first subchromosomal region; determining a first amount of DNA molecules located in the first subchromosomal region; determining a second amount of DNA molecules located in a second region; computing a count parameter from the first amount and the second amount; and comparing the count parameter to one or more count thresholds to determine the count classification of the type of aberration existing in the biological sample for the first subchromosomal region; determining, by the computer system, a size classification for the first subchromosomal region by: calculating a first statistical value of sizes of DNA molecules located in the first subchromosomal region; calculating a reference statistical value of sizes of DNA molecules located in a reference region; determining a separation value between the first statistical value and the reference statistical value; and comparing the separation value to one or more size thresholds to obtain the size classification; and calculating a first statistical value of sizes of DNA molecules located in the first subchromosomal region; calculating a reference statistical value of sizes of DNA molecules located in a reference region; determining a separation value between the first statistical value and the reference statistical value; and comparing the separation value to one or more size thresholds to obtain the size classification; and determining whether the fetus has the aberration in the first subchromosomal region based on the size classification and the count classification.