You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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.