fetch_clinvar_vcf
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.
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 |