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v0.1.0

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@rhshah rhshah released this 12 Jun 20:51
· 70 commits to main since this release
v0.1.0
e7aae8b

First release of vflank — variant-aware flanking-sequence extraction and masking for ddPCR assay design.

Features

  • Small variants (vflank small) — ±N bp flanks from a MAF, raw + masked FASTA, deduplicated per unique variant (CHR_POS_REF_ALT).
  • Fusions / SVs (vflank fusion) — reverse-complement-aware junction sequences from an iCallSV / iAnnotateSV breakpoint table (columns matched by name).
  • SNP masking, two backends — local gnomAD VCFs or the gnomAD GraphQL API (no download), each with --pop-data {genome,exome,both}.
  • Genome-build guard, flank-truncation detection, and a categorised skip summary + optional TSV report.

Install

pip install vflank
# or
docker run --rm ghcr.io/rhshah/vflank --help

Docs: https://rhshah.github.io/vFlank/

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