Applies the DuckHTS `duckdb_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-aligninbcftools +liftover.