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'''relativeFinder''' examines every pair of genotyped individuals in a pedigree. Then, it calculates the likelihood of the pair of the observed genotype data for the pair using the relationship specified in the pedigree and using a series of alternate relationships (described in a template pedigree file). If any of these alternate relationships makes the observed genotype data more likely, the pair is flagged.
'''relativeFinder''' examines every pair of genotyped individuals in a pedigree. Then, it calculates the likelihood of the pair of the observed genotype data for the pair using the relationship specified in the pedigree and using a series of alternate relationships (described in a template pedigree file). If any of these alternate relationships makes the observed genotype data more likely, the pair is flagged.
Before evaluating relationship likelihoods, relativeFinder will flag individuals with outlier patterns for heterozygosity or missing genotypes. To do this, relativeFinder checks whether the fraction of heterozygous sites or the total number of available genotypes differs froom the sample average by three standard deviations or more. Results for any flagged samples should be treated with caution, as problematic heterozygosity or missing data patterns can lead to odd results for the relativeFinder algorithm.
== Command Line Options ==
== Command Line Options ==
