1. A method for determining whether a male fetus of a pregnant female has an X-linked mutation, wherein the pregnant female is heterozygous for a mutant and a normal allele at a locus on the X chromosome, the method comprising: performing a plurality of reactions, each involving one or more nucleic acid molecules from a biological sample, the biological sample including cell-free nucleic acid molecules from the pregnant female and from the male fetus; detecting data from the plurality of reactions, receiving, by a computer system, the data from the plurality of reactions, wherein the data includes: a first set of quantitative data indicating a first amount of the mutant allele at the locus; and a second set of quantitative data indicating a second amount of the normal allele at the locus; determining, by the computer system, a parameter from the first amount and the second amount, wherein the parameter represents a relative amount between the first and second amounts; obtaining, by the computer system, a percentage Pf of fetal nucleic acid molecules in the biological sample; calculating, by the computer system, a first cutoff value for determining whether the fetus has inherited the mutant allele at the locus, wherein the first cutoff value is derived at least from a first proportion of k/(1+k−Pf), where k is a number of mutant alleles on a mutant chromosome of the pregnant female, k being an integer equal to or greater than one; calculating, by the computer system, a second cutoff value for determining whether the fetus has inherited the normal allele at the locus, wherein the second cutoff value is derived at least from a second proportion of [k(1−Pf)]/[1+k−kPf)]; and comparing, by the computer system, the parameter to at least one of the first and second cutoff values to determine a classification of whether the fetus has inherited the mutant allele or the normal allele.