Import an Already Selected Somalier Sites VCF or BCF — rduckhts_somalier_import

Convert an existing Somalier-compatible sites file into the canonical typed panel and population-frequency relation used by DuckHTS extraction, relatedness, and contamination functions. REF and ALT are oriented into lexical A/B order and alternate-allele frequency is flipped with the alleles, so `population_b_af` always describes `allele_b`. Exact Somalier v0.3.4 X/Y aliases are excluded, matching its autosomal frequency importer.

Usage

rduckhts_somalier_import_sites(
  con,
  path,
  assembly,
  max_sites = 1e+06,
  table_name = NULL,
  overwrite = FALSE
)

Arguments

con: A DuckDB connection with DuckHTS loaded.
path: One already selected sites VCF/BCF path or URI. `INFO/AF` must be declared `Number=A,Type=Float` and every retained record must be one canonical biallelic SNV with one finite AF value.
assembly: Nonempty assembly identifier attached to every site.
max_sites: Positive input-site limit, at most 100,000,000.
table_name: Optional output table. `NULL` returns a data frame.
overwrite: Whether an existing output table may be replaced.

Value

A data frame if `table_name` is `NULL`; otherwise invisible `TRUE`.

Details

This function does not select sites from a population VCF. Somalier's `find-sites` algorithm has separate AF/AN, QC, interval-exclusion, and spacing semantics and is not implied by importing its output.