Rduckvep

R front end for DuckVEP, a variant consequence engine for DuckDB with Ensembl VEP semantics.

The package bundles DuckVEP extension sources and builds them offline for the installed duckdb R package. It provides:

• rduckvep_connect() and rduckvep_load() for a DuckDB connection with the extension loaded;
• rduckvep_annotate() for annotation results as a data frame, and rduckvep_annotate_sql() for the SQL builder;
• rduckvep_haplotypes(), rduckvep_coding_calls() and rduckvep_coding_transcripts() for phased coding calls;
• wrappers for Ensembl model builders, transcript projection, model receipts, loss-of-function calls, breakend evidence and structural HGVS.

Model loading uses duckvep_model_load() through DBI on the caller's connection. Its relations can include temporary tables and uncommitted rows. See the project page for compatibility evidence, differences from VEP and worked examples.

con <- Rduckvep::rduckvep_connect()
# After loading a model and creating an events relation:
Rduckvep::rduckvep_annotate(con, "events", "model", hgvs = TRUE)
DBI::dbGetQuery(con, "SELECT function_name FROM duckdb_functions() WHERE function_name LIKE 'duckvep%'")

Install from a source clone with Rscript r/Rduckvep/bootstrap.R . followed by R CMD INSTALL r/Rduckvep. DuckHTS (Rduckhts) is optional for VCF/BCF input.