The libraries were paired-end sequenced (75bp + 35bp reads) on the SOLiD 5500xl (Life Technologies). The sequence reads were aligned to the human genome (build hg19/GRCh37) using Bioscope 1.3 (Life Technologies) that aligns in color-space. After alignment, quality control measures were implemented including dropping subjects with low mapped reads (<1 million) and fold enrichment (<365). Mean coverage across the targeted regions for each individual was 78X, with at least 10X coverage for 88.2% of the targeted regions, an average fold enrichment of 393.8, and 97.9% of baits covered. This level of coverage is very high for color space data, where two color call errors must occur by chance in adjacent positions before a single-nucleotide polymorphism (SNP) is incorrectly called and therefore should result in fewer base calling errors relative to equivalent coverage on other sequencing platforms (McKernan et al., 2009).
