A method for classifying a copy number variation in a cancer genome by comparing cancer fraction estimates calculated by two different techniques, the method comprising: (a) sequencing cell free DNA from a cancer test sample to provide sequence reads from cancer and somatic 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 cancer 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 cancer fraction in the cancer 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 cancer fraction value from the chromosome dose; (e) estimating cancer fraction in the cancer 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 cancer fraction value (i) using information from one or more polymorphisms exhibiting an allelic imbalance in the cancer and somatic nucleic acids of the cancer test sample, or (ii) 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 cancer fraction value to the second cancer fraction value and determining (i) whether the two cancer 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 cancer 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 cancer is a mosaic. (a) sequencing cell free DNA from a cancer test sample to provide sequence reads from cancer and somatic 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 cancer 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 cancer fraction in the cancer 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 cancer fraction value from the chromosome dose; (e) estimating cancer fraction in the cancer 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 cancer fraction value (i) using information from one or more polymorphisms exhibiting an allelic imbalance in the cancer and somatic nucleic acids of the cancer test sample, or (ii) 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 cancer fraction value to the second cancer fraction value and determining (i) whether the two cancer 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 cancer 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 cancer is a mosaic.