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vflank 0.6.0

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@rhshah rhshah released this 17 Jun 19:05

Added

  • VCF/BCF input for small variants (vflank small run variants.vcf.gz). The
    input format is auto-detected by extension — no new command or flag. Read
    sites-only; anchor-base REF/ALT is normalised to MAF [Start, End];
    multi-allelic records expand per ALT; symbolic/SV/BND alleles are skipped;
    gene/HGVS come best-effort from a VEP CSQ / SnpEff ANN field. --samples
    doesn't apply to a (sites-only) VCF and is ignored with a warning;
    vflank small inspect previews the normalised variants. New io/vcf.py
    (is_vcf_path, vcf_to_maf_coords, load_vcf); run_small accepts a VCF
    path too. SV-VCF (Delly CT / Manta–GRIDSS BND) remains a follow-up.