rduckhts_somalier_vcf_counts: Extract Panel-Aligned Counts from VCF or BCF

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

Extract Panel-Aligned Counts from VCF or BCF

Description

Produce the complete sample-by-panel count relation consumed by the Somalier-derived relatedness, contamination and sex functions. 'FORMAT/AD' must declare 'Number=R,Type=Integer'; A and B slots are matched by exact REF/ALT identity, and 'other' sums only the remaining declared-allele slots. Missing sites and unavailable AD remain rows with three NULL counts, distinct from measured zero depth. The panel can be any typed table/view or ordinary Parquet file with the canonical six panel identity columns.

Usage

rduckhts_somalier_vcf_counts(
  con,
  path,
  panel_table = NULL,
  panel_parquet = NULL,
  samples = NULL,
  filter_policy = c("pass_or_unapplied", "include_all", "error"),
  table_name = NULL,
  overwrite = FALSE
)

Arguments

con	A DuckDB connection with DuckHTS loaded.
path	One VCF/BCF path or URI.
panel_table	Name of the ordered panel table or view.
panel_parquet	Ordinary panel Parquet path, instead of 'panel_table'.
samples	Optional HTSlib sample selector: comma-separated inclusion, leading '^' exclusion, '"-"' for all, or '""' for none.
filter_policy	Record FILTER policy: '"pass_or_unapplied"' makes named failures unavailable, '"include_all"' uses their AD, and '"error"' rejects a selected panel record with a named failure. X/Y sites ignore the policy and always use their AD, as Somalier extraction does.
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'.

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