A method for classifying a copy number variation in a fetal genome by comparing fetal fraction estimates calculated by two different techniques, the method comprising: (a) sequencing cell free DNA from a maternal test sample to provide sequence reads from fetal and maternal nucleic acids, wherein the sequence reads are provided in an electronic format; (b) aligning the sequence reads to one or more bins from a reference sequence using a computing apparatus and thereby providing sequence tags corresponding to the sequence reads; (c) computationally identifying a number of those sequence tags that are from one or more bins by using the computing apparatus and determining that a first bin of interest in the fetus harbors a copy number variation wherein the first bin of interest is a first chromosome of interest, and wherein the first chromosome of interest is selected from a group consisting of chromosomes 1-22, X, and Y; (d) estimating fetal fraction in the maternal test sample by a first mode that uses information from the tags from the first bin of interest, wherein the first mode comprises (a) calculating the number of sequence tags from the first chromosome of interest and at least one normalizing chromosome sequence to determine a chromosome dose; and (b) calculating a first fetal fraction value from the chromosome dose; (e) estimating fetal fraction in the maternal test sample by a second mode that does not use information from the tags from the first bin of interest, wherein the second mode comprises calculating a second fetal fraction value (i) using information from one or more polymorphisms exhibiting an allelic imbalance in the fetal and maternal nucleic acids of the maternal test sample, (ii) determining the number of tags aligning to the X chromosome of male fetal and maternal nucleic acids of the maternal test sample, or (iii) determining the number of tags aligning to a second bin of the reference sequence, wherein the second bin is not the first bin of interest and wherein the second bin has been determined to harbor a copy number variation; and (f) comparing the first fetal fraction value to the second fetal fraction value and determining (i) whether the two fetal fraction values have a difference that is less than a defined threshold, thereby determining that the first bin of interest has a complete aneuploidy or (ii) whether the two fetal fraction values have a difference that is greater than the defined threshold, thereby determining that either the first bin of interest harbors a partial aneuploidy, or the fetus is a mosaic. (a) sequencing cell free DNA from a maternal test sample to provide sequence reads from fetal and maternal nucleic acids, wherein the sequence reads are provided in an electronic format; (b) aligning the sequence reads to one or more bins from a reference sequence using a computing apparatus and thereby providing sequence tags corresponding to the sequence reads; (c) computationally identifying a number of those sequence tags that are from one or more bins by using the computing apparatus and determining that a first bin of interest in the fetus harbors a copy number variation wherein the first bin of interest is a first chromosome of interest, and wherein the first chromosome of interest is selected from a group consisting of chromosomes 1-22, X, and Y; (d) estimating fetal fraction in the maternal test sample by a first mode that uses information from the tags from the first bin of interest, wherein the first mode comprises (a) calculating the number of sequence tags from the first chromosome of interest and at least one normalizing chromosome sequence to determine a chromosome dose; and (b) calculating a first fetal fraction value from the chromosome dose; (e) estimating fetal fraction in the maternal test sample by a second mode that does not use information from the tags from the first bin of interest, wherein the second mode comprises calculating a second fetal fraction value (i) using information from one or more polymorphisms exhibiting an allelic imbalance in the fetal and maternal nucleic acids of the maternal test sample, (ii) determining the number of tags aligning to the X chromosome of male fetal and maternal nucleic acids of the maternal test sample, or (iii) determining the number of tags aligning to a second bin of the reference sequence, wherein the second bin is not the first bin of interest and wherein the second bin has been determined to harbor a copy number variation; and (f) comparing the first fetal fraction value to the second fetal fraction value and determining (i) whether the two fetal fraction values have a difference that is less than a defined threshold, thereby determining that the first bin of interest has a complete aneuploidy or (ii) whether the two fetal fraction values have a difference that is greater than the defined threshold, thereby determining that either the first bin of interest harbors a partial aneuploidy, or the fetus is a mosaic.