Extract variants from a gdb based on a set of ranges

Extract variant IDs from a gdb based on a set of ranges.

extractRanges(object, ranges, padding = 250)

Arguments

object

a gdb object

ranges

Can be a data.frame, including at least 'CHROM','start', and 'end' columns or a GenomicRanges::GRanges object.

padding

Number of basepairs to extend the search region beyond the specified genomic ranges to capture variants where the reference allele (REF) overlaps the input ranges, but the POS of the variant falls outside the ranges. This accounts for variants where the REF allele spans multiple base pairs.