rduckhts_bcftools_norm: Normalize Variant Alleles with bcftools-style Semantics

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

Normalize Variant Alleles with bcftools-style Semantics

Description

Applies the DuckHTS 'duckhts_bcftools_norm(...)' table macro to rows from a SQL query or table expression. Input rows must expose chromosome, 1-based position, reference allele, and alternate allele columns. Alternate alleles may be supplied either as a comma-delimited 'VARCHAR' or as a 'VARCHAR[]' list, matching the common DuckDB representations used by plain tables and 'read_bcf(...)'.

Usage

rduckhts_bcftools_norm(
  con,
  query,
  fasta_ref,
  chrom_col = "chrom",
  pos_col = "pos",
  ref_col = "ref",
  alt_col = "alt",
  split_multiallelic = FALSE,
  end_pos_col = NULL,
  svlen_col = NULL,
  fasta_index_path = NULL,
  gzi_path = NULL
)

Arguments

con	A DuckDB connection with DuckHTS loaded
query	SQL query or table expression to normalize
fasta_ref	Path to the reference FASTA
chrom_col	Source chromosome column name
pos_col	Source 1-based position column name
ref_col	Source reference allele column name
alt_col	Source alternate allele column name ('VARCHAR' or 'VARCHAR[]')
split_multiallelic	If 'TRUE', split multiallelic sites before normalization so 'alt_normed' is emitted as 'VARCHAR' plus 'alt_index'. If 'FALSE' (default), keep sites intact and emit 'alt_normed' as 'VARCHAR[]'.
end_pos_col	Optional source column name containing an END-like 1-based end coordinate for symbolic deletions.
svlen_col	Optional source column name containing an SVLEN-like signed length for symbolic duplications.
fasta_index_path	Optional explicit '.fai' sidecar path.
gzi_path	Optional explicit '.gzi' sidecar path for bgzipped FASTA.

Value

A data frame with the original columns plus 'pos_normed', 'end_pos_normed', 'ref_normed', 'alt_normed', 'normed', and 'norm_status'. In split mode the result additionally includes 'alt_index'.

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