Import the official ClinVar flat reports as one tidy table — rclinvarbitration_import

Joins variant_summary and submission_summary directly in DuckDB. The resulting clinvar table has one scalar row per variation, allele, assembly location, decision, SCV submission, RCV accession, or allele-gene link, identified by record_kind. It is the same canonical table used by rclinvarbitration_import_xml(). Location rows retain source coordinates even when ClinVar does not provide a complete VCF tuple (for example some CNVs). clinvar_vcf contains only locations with a usable one-based position and non-missing REF/ALT.

Usage

rclinvarbitration_import_flat(
  con,
  submission_path,
  variant_path,
  release_id,
  parquet_path = NULL,
  assembly = c("GRCh38", "GRCh37"),
  profile_id = "default",
  submitter_exclusions = character()
)

Arguments

con: A DuckDB DBI connection.
submission_path: Official submission_summary*.txt.gz.
variant_path: Official variant_summary*.txt.gz.
release_id: Immutable source-release label stored with the imported rows and returned in the import receipt.
parquet_path: Optional new Parquet path for the same tidy table. The returned import receipt can be passed directly to rclinvarbitration_publish_ducklake().
assembly: One or both of "GRCh38" and "GRCh37". Both are imported by default; policy decisions are computed once, preferring GRCh38 as the coordinate source when both are present.
profile_id: Policy profile recorded on decision rows.
submitter_exclusions: Submitters excluded from the policy decision.

Value

Invisibly returns the table name, release identity, source paths and byte sizes, and row counts by record kind.

Details

This is the compact default substrate for ClinVarbitration and temporal analysis. XML import remains available for evidence absent from the flat reports, including richer attributable observations and XML-only text.