Schematic workflow for summarizing and quantifying contiguous homozygosity. Example 10-Mb region on chromosome 1 illustrating how observed patterns of homozygous segments are processed to create intersecting segment length matrix (ISLMcm), calculate extAUC, and define peaks and outlier peak regions. (a) Coordinates of homozygous segments with length ≥49 kb (regional MISL). (b) Intersecting segment lengths for each locus are combined into ISLMcm. (c) An intersecting segment length vector (ISLV) is extracted from the ISLM, the sign of the values reversed, and extAUC is calculated by integrating the area-under-the-curve of the empirical cumulative distribution function (ECDF) using those values. Dashed red lines mark interval of integration after masking. (d) extAUC peak detection and processing: peaks are detected from a smooth spline function applied to extAUC values, peaks with extreme peak heights selected (outlier peaks), and neighboring outlier peaks that are not well separated are merged into peak regions.
Johnson et al. Genome Biology 2011 12:R21 doi:10.1186/gb-2011-12-3-r21