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PLINK1 --tdt: transmission disequilibrium test over complete trios.
For each variant, over affected offspring whose two parents are both genotyped and Mendel-consistent, count the minor allele transmitted (T) and untransmitted (U) by heterozygous parents. The statistic is McNemar’s: CHISQ = (T-U)² / (T+U), 1 df, OR = T/U.
A1 is the minor allele by founder allele frequency (PLINK’s convention), which fixes the T/U orientation and the A1/A2 labels.