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Fig. 1 | BMC Bioinformatics

Fig. 1

From: Simulating autosomal genotypes with realistic linkage disequilibrium and a spiked-in genetic effect

Fig. 1

A schematic drawing of the resampling procedure. Triads from three different families are shown in different colors. The solid bars represent the original GWAS subjects and open bars represent their corresponding complements. The triads used by our resampling algorithm include both case and complement triads. Break points are introduced at random and kept the same for the mother, father, and child genotypes across the mix of all observed and complement triads. Each chromosome is broken into several fragments with a mother-father-child triplicate fragment from a given chromosomal location treated as a unit. For each sequential location along the chromosome, one forms a location-specific fragment pool consisting of all the triplicate fragments from that location. A simulated triad is created by randomly sampling a triplicate fragment from each location-specific fragment pool in turn and then sequentially splicing the sampled fragments to make simulated chromosomes. The entire process of creating location-specific fragment pools is repeated for each subsequent simulated triad, starting with a new random set of breakpoints so that every simulated triad is based on a distinct fragmentation pattern

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