Query VCF/BCF with DuckDB

Enables SQL queries on VCF files using DuckDB. This allows powerful filtering, aggregation, and joining operations.

Usage

vcf_query_arrow(vcf_files, query, ...)

Arguments

vcf_files

Character vector of VCF file paths

query

SQL query string. Use "vcf" as the table name.

...

Additional arguments passed to vcf_open_arrow

Value

Query result as a data frame

Examples

if (FALSE) { # \dontrun{
# Count variants per chromosome
vcf_query_arrow(
  "variants.vcf.gz",
  "SELECT CHROM, COUNT(*) as n FROM vcf GROUP BY CHROM"
)

# Filter high-quality variants
vcf_query_arrow(
  "variants.vcf.gz",
  "SELECT * FROM vcf WHERE QUAL > 30"
)

# Join multiple VCF files
vcf_query_arrow(
  c("sample1.vcf.gz", "sample2.vcf.gz"),
  "SELECT * FROM vcf WHERE POS BETWEEN 1000 AND 2000"
)
} # }