Usage

Currently, AnyVLM is used primarily by issuing requests against an HTTP server. This page assumes that such a server is running at http://localhost:8080/.

Submitting VCFs

Given a VCF describing cohort-level allele frequency, submit a POST request to /ingest_vcf:

% curl -X POST "http://localhost:8080/ingest_vcf?assembly=grch38" \
  -F "file=@/path/to/variants.vcf.gz"

VCF Requirements

• File must be gzip-compressed (.vcf.gz)

• Maximum file size: 5GB

• Required INFO fields: AC, AN, AC_Het, AC_Hom, AC_Hemi

Response

After ingestion is complete, a simple response message will confirm success:

{
  "status": "success",
  "message": "Successfully ingested variants.vcf.gz",
  "details": null
}

Retrieving CAFs

Issue a GET request to /variant_counts with arguments for reference sequence, chromosome, position, and referance/alternate bases, like so:

% curl "http://localhost:8080/variant_counts?assemblyId=GRCh38&referenceName=22&start=10510105&referenceBases=T&alternateBases=A"

Parameters

Parameter	Description	Example
assemblyId	Reference assembly	"GRCh37", "GRCh38", "hg19", "hg38"
referenceName	Chromosome	1-22, X, Y, MT
start	Position (1-based)	44389414
referenceBases	Reference allele	A, ACGT, etc.
alternateBases	Alternate allele	G, TGCA, etc.

Response

The AnyVLM server will respond to a valid request with a VLM protocol-compliant JSON object that includes the following fields:

• beaconHandovers: Handover metadata for network integration, describing the data

• meta: Beacon metadata, describing the server itself

• responseSummary: Whether variant exists, and total number of matching results

• response: ResultSets grouped by zygosity (Homozygous, Heterozygous, Hemizygous, Unknown)

For example:

{
  "beaconHandovers": [
    {
      "handoverType": {
        "id": "GREGoR-NCH",
        "label": "GREGoR AnyVLM Reference"
      },
      "url": "https://variants.gregorconsortium.org/"
    }
  ],
  "meta": {
    "apiVersion": "v1.0",
    "beaconId": "org.anyvlm.gregor",
    "returnedSchemas": [
      {
        "entityType": "genomicVariant",
        "schema": "ga4gh-beacon-variant-v2.0.0"
      }
    ]
  },
  "responseSummary": {
    "exists": true,
    "numTotalResults": 2
  },
  "response": {
    "resultSets": [
      {
        "exists": true,
        "id": "GREGoR-NCH Homozygous",
        "results": [],
        "resultsCount": 2,
        "setType": "genomicVariant"
      },
      {
        "exists": true,
        "id": "GREGoR-NCH Heterozygous",
        "results": [],
        "resultsCount": 0,
        "setType": "genomicVariant"
      },
      {
        "exists": true,
        "id": "GREGoR-NCH Hemizygous",
        "results": [],
        "resultsCount": 0,
        "setType": "genomicVariant"
      }
    ]
  }
}

GA4GH Service Info

AnyVLM also supports the GA4GH Service Info Specification. A GET request to /service-info returns GA4GH-compliant service metadata.