Export ClinVarbitration decisions to Parquet — rclinvarbitration_export_clinvarbitration

schema = "compatibility" 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.

Usage

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

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.
schema: Output schema: the upstream-compatible seven-column relation or the canonical scalar evidence relation.

Value

A named list describing the written Parquet file, invisibly.

Details

schema = "tidy" writes the canonical scalar clinvar relation. record_kind distinguishes variations, alleles, assembly locations, source assertions, conditions, genes, observations, citations, text, attributes, allele policy decisions, and disease-level disease_decision policy rows. Every row has its own stable record_key; repeated source elements are rows rather than lists or structs. release_id is a required Parquet column, so a reopened export retains its source identity.

The compatibility source is the allele-level policy view joined through clinvar_vcf. Both GRCh37 and GRCh38 are supported, including distinct X/Y locations for one AlleleID. Primary NC_ placements take precedence when present. An allele available only on alternate placements retains its exact sequence accession and is not mislabeled as a primary-chromosome VCF record.

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.