variantgrid_api
Python API client for VariantGrid Open source Variant database and analysis platform
See changelog
Install
python3 -m pip install variantgrid_api
Example
from variantgrid_api.api_client import VariantGridAPI
from variantgrid_api.data_models import EnrichmentKit
api = VariantGridAPI(server="https://variantgrid.com", api_token="YOUR_API_TOKEN")
enrichment_kit = EnrichmentKit(name="idt_haem", version=1)
result = api.create_enrichment_kit(enrichment_kit)
Annotate a VCF and download it back
Upload a VCF, wait for VariantGrid to import + annotate any novel variants, then download the cohort-level annotated export (all samples, single-sample VCFs included). The whole flow is a one-liner:
from variantgrid_api.api_client import VariantGridAPI
api = VariantGridAPI(server="https://variantgrid.com", api_token="YOUR_API_TOKEN")
# export_type is "vcf" (gzipped *.vcf.gz) or "csv" (zipped *.csv.zip)
path = api.annotate_vcf("input.vcf", export_type="vcf", dest_path="/data/results/")
print(f"Annotated VCF written to {path}")
There's also a vg_api annotate_vcf command line tool (first call uploads, run it again to download once
ready), a step-by-step form (upload_file → wait_for_annotation → download_annotated), and a "submit now,
download later" pattern for long-running jobs. See
Annotate a VCF on the wiki.
Testing
# Install required testing packages
python3 -m pip install -e ".[test]"
python3 -m pytest --cov=variantgrid_api
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