Count variants in a VCF/BCF file — vcf_count_duckdb • RBCFTools

Fast variant count using DuckDB projection pushdown.

Usage

vcf_count_duckdb(
  file,
  extension_path = NULL,
  region = NULL,
  tidy_format = FALSE,
  con = NULL
)

Arguments

file: Path to VCF, VCF.GZ, or BCF file
extension_path: Path to the bcf_reader.duckdb_extension file.
region: Optional genomic region for indexed files
tidy_format: Logical, if TRUE counts rows in tidy format (one per variant-sample). Default FALSE returns count of variants.
con: Optional existing DuckDB connection (with extension loaded).

Value

Integer count of variants (or variant-sample combinations if tidy_format=TRUE)

Examples

if (FALSE) { # \dontrun{
ext_path <- bcf_reader_build(tempdir())
vcf_count_duckdb("variants.vcf.gz", ext_path)
vcf_count_duckdb("variants.vcf.gz", ext_path, region = "chr22")

# Count variant-sample rows (variants * samples)
vcf_count_duckdb("cohort.vcf.gz", ext_path, tidy_format = TRUE)
} # }