SNP data

SNP data in standard VCF format. Target genomic intervals for variant calling were identified using GATK’s CallableLoci. To avoid spurious calls at the edges of the RRBS target regions, the target intervals were trimmed by three bases on each end. Bwa-meth was used to align the reads for input to Bis-SNP. Bis-SNP’s BisulfiteGenotyper was run with the following parameters: -stand_call_conf 4 -stand_emit_conf 0 –maximum_read_cov 100000 –mm40 10 –trim5 2 –trim3 2 –mmq 10 –mbq 15 –useBAQ. GATK’s VariantFiltration and SelectVariants were used to remove calls for sites with low depth of coverage (DP < 4), restrict to diallelic sites, and filter variants based on the following GATK variant annotation cutoffs, QD < 2.0, MQ < 40.0, MQRankSum < −12.5, ReadPosRankSum < −8.0, and AF < 0.1.