Build a shared master heterozygous-SNP list across donors

Reads donor VCFs once and returns a sorted, de-duplicated GRanges of biallelic heterozygous SNPs spanning all requested donors. The returned object carries, per site, the set of donors heterozygous there ($donorMembership, a CharacterList), so the donor mask can be applied later without re-reading VCFs. Save this once and pass it to DsASC.gatk(..., masterGr = ) in each per-cell-type job to keep all objects row-aligned.

buildMasterSNPs(donors, vcfDir, genome)

Arguments

donors

Character vector of donor IDs.

vcfDir

Directory with {donor}_heterozygous.vcf.gz files.

genome

Genome assembly string (e.g. "hg38").

Value

A GRanges with REF, ALT, snpId, donorMembership metadata; names() = snpId.