The variants were called and filtered using GATK (McKenna et al., 2010) according to best practices recommendations (Van der Auwera et al., 2013, DePristo et al., 2011). Specifically, we employed variant quality score recalibration to filter variants. We defined rare variants as having a minor allele frequency (MAF) < 0.01 and common variants as MAF ≥ 0.01.
