Export an allele-level ClinVarbitration-compatible Parquet file — rclinvarbitration_export_clinvarbitration

Writes the seven columns in Centre for Population Genomics ClinVarbitration's clinvar_decisions.tsv: contig, position, reference, alternate, clinical_significance, gold_stars, and allele_id. The source is the package's allele-level policy view, not the disease-level decision view, so each output row is usable as a locus/alleles annotation record. Both GRCh37 and GRCh38 are supported. The output retains every qualifying source locus, including distinct X/Y locations for one AlleleID.

Usage

rclinvarbitration_export_clinvarbitration_parquet(
  con,
  path,
  release_id,
  assembly = c("GRCh38", "GRCh37"),
  profile_id = "default",
  submitter_exclusions = character()
)

Arguments

con: A DuckDB DBI connection initialized with rclinvarbitration_init().
path: New output .parquet file path.
release_id: Imported ClinVar release label to export.
assembly: Genome assembly: "GRCh38" or "GRCh37".
profile_id: Policy profile identifier, normally "default".
submitter_exclusions: Additional submitter names to exclude from this export. Matching is case-insensitive and ignores surrounding whitespace. These exclusions are combined with any exclusions already stored for profile_id; imported source submissions are not deleted.

Value

A named list describing the written Parquet file, invisibly.

Details

The file is schema-compatible with the upstream TSV/Hail decision resource, but is not claimed to be byte-for-byte equivalent: this package derives submissions and locations from VCV XML, whereas upstream uses ClinVar's tab-delimited submission and variant summaries. PM5 is deliberately not exported; Rduckhts/DuckHTS own downstream consequence and PM5 processing.