This function imports ASC data by counting reads at heterozygous SNP sites
defined in donor-specific VCF files. It uses Rsamtools::pileup to
quantify reference and alternative alleles.
DsASC.gatk(sampleAnnot, vcfDir, genome, diskDump = FALSE, masterGr = NULL)Data frame with sample annotation. Must contain 'sampleId', 'bamFilename', 'donor'.
Directory containing donor VCFs named {donor}_heterozygous.vcf.gz.
Character string containing genome assembly (e.g. "hg38").
Logical. If TRUE, matrices are realized as HDF5 arrays.
Optional pre-built master SNP GRanges (from
buildMasterSNPs). If supplied, the per-VCF master
construction is skipped and counts are stored against this
shared site set. Use this so per-cell-type objects built in
separate jobs remain row-aligned for cross-cell-type
comparison (Fig 4d). Must carry REF, ALT, snpId metadata and
names() set to snpId (as buildMasterSNPs produces).
A DsASC object.
Counts are stored against a union ("master") SNP list spanning all donors, but each sample is counted ONLY at sites heterozygous in its own donor. Sites outside a sample's donor het set are set to NA so they are never tested (prevents homozygous genotypes from being mis-called as allele-specific).