fetch_clinvar_vcf
Read-only
Read one region of ClinVar's monthly release VCF, as the VCF ClinVar publishes: its header, then every record overlapping the region, through the release's tabix index so only those blocks are fetched. The ID column is the ClinVar Variation ID and INFO carries ClinVar's own CLNSIG, CLNREVSTAT and CLNDN. Use it to put ClinVar's calls for a locus beside your own.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| end | Yes | last base of the region (1-based, inclusive). | |
| chrom | Yes | the chromosome, with or without its chr prefix. | |
| start | Yes | first base of the region (1-based). | |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| assembly | No | which release VCF to read. | GRCh38 |
| max_records | No | cap on records returned; the result says when the region held more. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| vcf | Yes | ClinVar's header and the region's records, as the file holds them | |
| records | Yes | how many records the region returned | |
| summary | Yes | which release was read, and how many records the region held | |
| fileDate | Yes | the release's own ##fileDate, which names the release read | |
| endpoints | Yes | the VCF and index URLs actually read | |
| truncated | Yes | whether the region held more records than max_records |