Produce the complete sample-by-panel count relation consumed by the Somalier-derived relatedness and contamination 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.
- table_name
Optional output table. `NULL` returns a data frame.
- overwrite
Whether an existing output table may be replaced.