In the T2D HPFS project, all subjects are male, but several HapMap females were genotyped as controls for the gender identity check. Figure 1 shows one HapMap female (a cell line sample) that appears to be XX/XO. The plot also shows five unusual males with low Y intensity and substantial levels of X heterozygosity, while all other males have zero heterozygosity. This situation is an artifact of the Birdseed method for calling X chromosome genotypes. In this algorithm, samples inferred to be males by annotation and/or Y chromosome intensity are analyzed with a prior assumption of two genotype clusters, while those inferred to be females have a prior assumption of three clusters. Based on their low Y intensities, these five males were mis-assigned as females during automated calling of the X chromosome genotypes. Consequently, the X chromosome SNPs of these five samples are flagged for omission from association analyses.
