A computer-implemented 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: identifying a location of the DNA molecule by comparing sequence information of the DNA molecule with a reference genome, thereby obtaining locations of the plurality of DNA molecules; for each of a plurality of non-overlapping bins in the reference genome: determining a respective amount of the plurality of DNA molecules located in the respective non-overlapping bin using the locations of the plurality of DNA molecules, computing a respective bin count parameter from the respective amount, and comparing the respective bin count parameter to one or more bin count thresholds to determine a bin count classification of a type of aberration of the respective non-overlapping bin; performing a segmentation process that merges consecutive non-overlapping bins into a merged segment based on the consecutive non-overlapping bins having a same bin count classification; comparing a length of the merged segment to a length threshold; computing a count parameter for the merged segment from the bin count parameters of the non-overlapping bins of the merged segment or from the amounts of the plurality of DNA molecules located in the non-overlapping bins of the merged segment; comparing the count parameter to one or more deviation thresholds to determine a count classification of the type of aberration; and determining whether the fetus has the aberration in a subchromosomal region corresponding to the merged segment based on the comparison of the length of the merged segment to the length threshold and the count classification, wherein the fetus is determined to have the aberration when the length of the merged segment exceeds the length threshold and the count classification indicates the aberration. for each of a plurality of DNA molecules in the biological sample: identifying a location of the DNA molecule by comparing sequence information of the DNA molecule with a reference genome, thereby obtaining locations of the plurality of DNA molecules; for each of a plurality of non-overlapping bins in the reference genome: determining a respective amount of the plurality of DNA molecules located in the respective non-overlapping bin using the locations of the plurality of DNA molecules, computing a respective bin count parameter from the respective amount, and comparing the respective bin count parameter to one or more bin count thresholds to determine a bin count classification of a type of aberration of the respective non-overlapping bin; determining a respective amount of the plurality of DNA molecules located in the respective non-overlapping bin using the locations of the plurality of DNA molecules, computing a respective bin count parameter from the respective amount, and comparing the respective bin count parameter to one or more bin count thresholds to determine a bin count classification of a type of aberration of the respective non-overlapping bin; performing a segmentation process that merges consecutive non-overlapping bins into a merged segment based on the consecutive non-overlapping bins having a same bin count classification; comparing a length of the merged segment to a length threshold; computing a count parameter for the merged segment from the bin count parameters of the non-overlapping bins of the merged segment or from the amounts of the plurality of DNA molecules located in the non-overlapping bins of the merged segment; comparing the count parameter to one or more deviation thresholds to determine a count classification of the type of aberration; and determining whether the fetus has the aberration in a subchromosomal region corresponding to the merged segment based on the comparison of the length of the merged segment to the length threshold and the count classification, wherein the fetus is determined to have the aberration when the length of the merged segment exceeds the length threshold and the count classification indicates the aberration.