rduckhts_somalier_import_sites: Import an Already Selected Somalier Sites VCF or BCF

In Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension

Import an Already Selected Somalier Sites VCF or BCF

Description

Convert an existing Somalier-compatible sites file into the canonical typed panel and population-frequency relation used by DuckHTS extraction, relatedness, contamination, and sex 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'. Records on the exact Somalier v0.3.4 X/Y aliases are kept as sex-chromosome sites, numbered after every autosomal site; relatedness and contamination functions ignore them and 'rduckhts_somalier_sex()' reads them. No pseudo-autosomal filtering happens on import or extraction, as in Somalier: select X sites outside the PAR when choosing the sites file. At least one autosomal record is required.

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.

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.

Value

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

Rduckhts documentation built on Oct. 25, 2026, 1:08 a.m.