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Annotate a VCF from the command line

Installing the package (pip install variantgrid_api) gives you a vg_api command. Submit a VCF for annotation, then run the same command again to download it once it's ready - no state to keep, since uploads are keyed on the file's SHA-256:

$ export VARIANTGRID_API_TOKEN=YOUR_API_TOKEN
$ vg_api annotate_vcf input.vcf.gz -o results/
Uploaded input.vcf.gz (id=13256).
Annotating input.vcf.gz - run the same command again later to download.

$ vg_api annotate_vcf input.vcf.gz -o results/        # once it's done
Annotated vcf written to results/input.vcf_annotated_v254_GRCh38.vcf.gz

See Annotate a VCF for the full guide - batches, the Python API, and all the options.

Guides

• Annotate a VCF - upload a VCF, annotate it, and download the annotated export