Fig. 1
From: EM-mosaic detects mosaic point mutations that contribute to congenital heart disease
Mosaic detection pipeline flowchart. Summary of approach for detecting mosaic variants in our cohort of n = 2530 CHD proband-parent trios. EM-mosaic flowchart (left). We first processed our SAMtools de novo calls using our upstream filters (n = 2396 sites passing all filters). We then applied the same upstream filters to the published dnSNVs from Jin et al. (n = 2650 sites passing all filters) before finally taking the union of these two call sets (n = 3192). High-confidence mosaics (n = 309) were defined as mosaics passing IGV inspection and having posterior odds > 10. Italicized text indicates which filters removed candidate mosaic variants called by MosaicHunter but not by EM-mosaic. MosaicHunter workflow (right). Quality control filters excluded any sites that were (1) present in ExAC (2) G>T with Nalt < 10 (3) parent Nalt > 2. Outliers were defined as probands carrying more than 20 mosaics, or non-unique sites. We also removed sites called as germline by GATK Haplotype Caller. High-confidence mosaics (n = 116) were defined as having a likelihood ratio > 80 and affecting coding regions excluding MUC/HLA genes. Italicized text indicates which filters removed variants called by EM-mosaic but not by MosaicHunter