## Additional file 2.
χ^{2}(1) distribution. The first three columns correspond to the Armitage trend test statistic
computed using the true genotypes (True), called genotypes without filtering (Call
NF), and called genotypes with filtering (Call F), respectively. The fourth column
corresponds to the likelihood ratio test statistic with unknown minor allele (LRT).
Assuming 500 cases and 500 controls, under the null hypothesis, a set of 5,000 sites
were simulated with a MAF of 5% with a sequencing depth of 2× (upper panels) and 5×
(lower panels). The "Inflation" factor [44] is shown in the upper left corner of each figure.
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