A method for determining the presence or absence of a genetic variation, comprising: (a) amplifying in a single reaction a plurality of sets of paralogous polynucleotide species from nucleic acid in a sample, the amplifying comprising contacting the nucleic acid with a plurality of amplification primers under amplification conditions to obtain a plurality of amplified sets of paralogous polynucleotide species, wherein (i) each set of the plurality of amplified sets of paralogous polynucleotide species includes paralogous polynucleotide species located on a target chromosome and one or more reference chromosomes; and (ii) each set of the plurality of paralogous polynucleotide species is amplified by a different single pair of amplification primers of the plurality of amplification primers and each primer of the plurality of amplification primers is complementary to less than 20 positions in a human genome; (b) determining, for each set of the plurality of amplified sets of paralogous polynucleotide species the amount of the paralogous polynucleotide species from the target chromosome and the amount of the paralogous polynucleotide species from the one or more reference chromosomes; (c) determining, for each set of the plurality of amplified sets, a paralog ratio between the amount of the paralogous polynucleotide species from the target chromosome and the amount of the paralogous polynucleotide species from the one or more reference chromosomes; (d) determining, for the paralog ratio determined for each set of the plurality of amplified sets of paralogous polynucleotide species, a z-score; (e) determining, for the sample, a sample z-score based on the z-score determined for each set of the plurality of amplified sets of paralogous polynucleotide species; and (f) determining, for the sample, the presence or absence of the genetic variation based on the sample z-score. (a) amplifying in a single reaction a plurality of sets of paralogous polynucleotide species from nucleic acid in a sample, the amplifying comprising contacting the nucleic acid with a plurality of amplification primers under amplification conditions to obtain a plurality of amplified sets of paralogous polynucleotide species, wherein (i) each set of the plurality of amplified sets of paralogous polynucleotide species includes paralogous polynucleotide species located on a target chromosome and one or more reference chromosomes; and (ii) each set of the plurality of paralogous polynucleotide species is amplified by a different single pair of amplification primers of the plurality of amplification primers and each primer of the plurality of amplification primers is complementary to less than 20 positions in a human genome; (i) each set of the plurality of amplified sets of paralogous polynucleotide species includes paralogous polynucleotide species located on a target chromosome and one or more reference chromosomes; and (ii) each set of the plurality of paralogous polynucleotide species is amplified by a different single pair of amplification primers of the plurality of amplification primers and each primer of the plurality of amplification primers is complementary to less than 20 positions in a human genome; (b) determining, for each set of the plurality of amplified sets of paralogous polynucleotide species the amount of the paralogous polynucleotide species from the target chromosome and the amount of the paralogous polynucleotide species from the one or more reference chromosomes; (c) determining, for each set of the plurality of amplified sets, a paralog ratio between the amount of the paralogous polynucleotide species from the target chromosome and the amount of the paralogous polynucleotide species from the one or more reference chromosomes; (d) determining, for the paralog ratio determined for each set of the plurality of amplified sets of paralogous polynucleotide species, a z-score; (e) determining, for the sample, a sample z-score based on the z-score determined for each set of the plurality of amplified sets of paralogous polynucleotide species; and (f) determining, for the sample, the presence or absence of the genetic variation based on the sample z-score.