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

ABSTRACT: 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.

INSTRUMENT(S): -

ORGANISM(S): Homo Sapiens

SUBMITTER: The University of Sydney

PROVIDER: PRJEB94535 | EVA | 2025-08-12

REPOSITORIES: EVA

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Dataset's files

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			Action	DRS
	AncestryMarkers_255samples_LDPruned.vcf.csi	Other
	AncestryMarkers_255samples_LDPruned.vcf.gz	Vcf
	AncestryMarkers_255samples_LDPruned.vcf.gz.csi	Vcf
	epic_germline_b2_99_AC_AF.vcf.csi	Other
	epic_germline_b2_99_AC_AF.vcf.gz	Vcf

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