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vflank

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Variant-aware flanking-sequence extraction and masking for ddPCR assay design.

vflank takes genomic variants — small variants (SNPs/indels) and structural variants (fusions) — and produces the sequence a ddPCR assay is designed around: the flanks of each variant (or the chimeric junction of a fusion), with common polymorphisms masked so primers and probes avoid them.

It is the front-end of an assay-design pipeline. It does not design primers itself — it prepares clean, masked target sequences to hand to a designer.

flowchart LR
    MAF["MAF
small variants"] --> FL
    BP["Breakpoints
fusions / SVs"] --> FL
    REF[("Reference
FASTA / API")] --> FL
    POP[("gnomAD
VCF / API")] --> MK
    BAM[("Sample BAM
optional")] --> MK
    subgraph vflank["vflank · front-end"]
        direction LR
        FL["Extract flanks /
build junction"] --> MK["Mask common SNPs
+ patient consensus"]
    end
    MK --> OUT["Raw + Masked
FASTA"]
    OUT --> OL["Olivar
amplicons"] --> DD["ddPCR assays"]
    OUT --> P3["Primer3
junction probes"] --> DD
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Highlights

  • Small variants — extract ±N bp flanks from a MAF, emit raw + masked FASTA records, deduplicated per unique variant (CHR_POS_REF_ALT).
  • Fusions / SVs — build the reverse-complement-aware junction sequence from a breakpoint table (iCallSV / iAnnotateSV format).
  • SNP masking, two ways — local gnomAD VCFs or the gnomAD GraphQL API (no download), each with genome / exome / both.
  • Reference, two ways — a local indexed FASTA or the UCSC API (--ref-source api, no download).
  • No silent failures — build-mismatch guard, flank truncation detection, and a categorised skip summary.

Install

pip install vflank                                    # released versions, from PyPI
pip install git+https://github.com/rhshah/vFlank.git  # latest from GitHub

See Installation and the Quick Start.

At a glance

# Small variants: flanks + masking via the gnomAD API (no download)
vflank small run variants.maf -r GRCh37.fasta -g hg19 --pop-source api

# Fusions: junction sequences from a breakpoint table
vflank fusion run breakpoints.tsv -r GRCh37.fasta -g hg19

Scope

vflank stops at the prepared target sequence. Downstream, those sequences feed a primer/probe designer (e.g. Primer3 for fusion-junction probes). See the Architecture for the full picture and roadmap.