Web tool

There is a hosted web front-end for vflank — an editable grid where you paste one variant (or a small batch) and get back the masked target sequence, no install required:

Open the web app

It is a thin layer over this library: the browser app calls vflank.run_small / run_fusion and renders the result. All the science — flank extraction, junction building, SNP masking — lives here in vflank. The web tool is scoped to the no-download path (UCSC reference + gnomAD APIs, modes A/B): single variants or tiny batches (≤10), no BAM, no PHI. For BAM consensus, large batches, or scripting, use the CLI or the Python API.

First load may be slow

The app is hosted on a free tier that sleeps after ~15 minutes of inactivity, so the first request after a while can take ~30 s to wake. Once it is up it is responsive.

Small variant

Paste a variant (here, BRAF V600E on GRCh37), press Run, and vflank pulls the reference from UCSC and common SNPs from gnomAD — nothing is downloaded — and returns the flanking sequence with the variant and common SNPs masked. Download the FASTA or a Primer3 input.

Fusion

Switch to Fusion and enter the two breakpoints (here, EML4–ALK). vflank builds the chimeric junction a probe spans, masks common SNPs in the flanks so the probe avoids them, and returns the junction sequence to download.

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The web app is a separate repository — rhshah/vFlank-webapp — and pins a released vflank. See its README to run it locally or deploy your own.