rduckhts_liftover: Lift Over Variant Coordinates Against a Query
In Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension

rduckhts_liftover

R Documentation

Lift Over Variant Coordinates Against a Query

Description

Applies the DuckHTS 'duckhts_liftover(...)' table macro to rows from a SQL query or table expression with chromosome and position columns, plus optional reference and alternate alleles.

Usage

rduckhts_liftover(
  con,
  query,
  chain_path,
  dst_fasta_ref,
  chrom_col = "chrom",
  pos_col = "pos",
  ref_col = NULL,
  alt_col = NULL,
  src_fasta_ref = NULL,
  max_snp_gap = 1,
  max_indel_inc = 250,
  lift_mt = FALSE,
  end_pos_col = NULL,
  no_left_align = FALSE
)

Arguments

`con`	A DuckDB connection with DuckHTS loaded
`query`	SQL query or table expression to lift over
`chain_path`	Path to a UCSC chain file
`dst_fasta_ref`	Path to the destination FASTA reference
`chrom_col`	Source chromosome column name
`pos_col`	Source 1-based position column name
`ref_col`	Optional reference allele column name
`alt_col`	Optional alternate allele column name
`src_fasta_ref`	Optional source FASTA reference
`max_snp_gap`	Maximum chain block merge gap
`max_indel_inc`	Maximum indel anchor expansion
`lift_mt`	If FALSE (default), mitochondrial variants with matching source/destination contig lengths are passed through with only contig rename. If TRUE, MT variants are lifted through the chain like any other contig.
`end_pos_col`	Optional column name containing INFO/END positions (1-based) to lift alongside the primary position. When provided, the output includes a 'dest_end' column with the lifted end position.
`no_left_align`	If FALSE (default), lifted indels are left-aligned against the destination reference. Set TRUE to skip left-alignment, mirroring `--no-left-align` in `bcftools +liftover`.