Development of a southern African-relevant methylome-wide EPIC filtering resource for SNP-confounded probe removal

A southern African-relevant variant filtering resource was generated using high-coverage (mean 43X) whole genome sequencing data from 99 genetically confirmed southern African individuals. Germline single nucleotide variants (SNVs) and small insertions/deletions (<50 bp) were called against the GRCh38 reference genome, and variants with a minor allele frequency (MAF) >0.01 were retained to create a population-specific filter optimised for downstream genomic analyses in southern African cohorts. Ancestry markers used to determine the ancestry of these 99 individuals and an additional 192 individuals are included.