Fig. 1.

Comparison of PMD identification methods. a Comparison of PMD estimates from all three methods on chromosome 6 for three samples with substantial variation in PMD depth. b Pairwise Jaccard index distributions comparing within-cancer-type and between-cancer-type for PMD sets identified using each method. c Pairwise Jaccard index heatmaps of TCGA cancer sample PMDs identified by each method. d Effect of downsampling and low coverage on PMD estimates. e Jaccard index of downsampled PMD estimates with their respective full-coverage sample for all human PMD-containing samples