Issues

• Track VEP 116.0 bugs that vepyr reproduces for parity (fix after 0.11.0)

  bug
  biodatageeks/vepyr#269 · Filter by author mwiewior opened on Oct 30, 2026
  1

• perf: ClinVar annotates ~20x slower per record than HG002; chr2 single-partition tail dominates wall time

  enhancement
  biodatageeks/vepyr#258 · Filter by author mwiewior opened on Oct 20, 2026
  1

• perf: 8-worker grid_plans +6% with formats 2d94421 (likely #267/#269 ensembl-cache provider), found on #251

  bug
  biodatageeks/vepyr#257 · Filter by author mwiewior opened on Oct 20, 2026
  1

• VCF output: carry raw INFO/FORMAT text through so unreserved and lower-case escapes round-trip (#207 follow-up)

  biodatageeks/vepyr#252 · Filter by author mwiewior opened on Oct 18, 2026

• VEP 116.2 support: extTer HGVSp rule and a 116.2 release target (builds on #50, #51)

  enhancement
  biodatageeks/vepyr#203 · Filter by author mwiewior opened on Oct 18, 2026
  1

• buffer_size only changes output on merged/RefSeq caches

  documentationenhancement
  biodatageeks/vepyr#141 · Filter by author mwiewior opened on Sep 29, 2026
  1

• output_vcf ignores check_existing / af* / max_af / pubmed unless everything=True

  biodatageeks/vepyr#123 · Filter by author mwiewior opened on Sep 20, 2026

• VCF shard tempdir name collides at workers>1: 'File exists (os error 17)'

  bug
  biodatageeks/vepyr#99 · Filter by author mwiewior opened on Sep 9, 2026

• everything=True without reference_fasta refuses — VEP demotes the implied --hgvs and carries on

  bug
  biodatageeks/vepyr#98 · Filter by author mwiewior opened on Sep 9, 2026

• One malformed VCF record aborts the whole run — VEP skips it with a warning and carries on

  bug
  biodatageeks/vepyr#96 · Filter by author mwiewior opened on Sep 9, 2026

• CSQ header declares 74 field names without everything=True — VEP declares 23

  bug
  biodatageeks/vepyr#94 · Filter by author mwiewior opened on Sep 9, 2026

• regulatory/motif annotation is unconditional — VEP gates it behind --regulatory

  bugenhancementfuture-improvement
  biodatageeks/vepyr#92 · Filter by author mwiewior opened on Sep 9, 2026

• Plugin-only annotation: emit VEP's core @DEFAULT_OUTPUT_COLS plus plugin fields (fields="core")

  biodatageeks/vepyr#72 · Filter by author mwiewior opened on Sep 4, 2026

• plugins= records the temporary subset root in the output VCF's provenance header

  biodatageeks/vepyr#59 · Filter by author mwiewior opened on Aug 29, 2026

• Plugin annotations are unusable from the DataFrame path: unnamed inside CSQ, dropped by default skip_csq

  biodatageeks/vepyr#57 · Filter by author mwiewior opened on Aug 29, 2026

• Release identity gate has no 116.1 target (supported_vep_targets)

  biodatageeks/vepyr#51 · Filter by author sitekwb opened on Aug 25, 2026

• HGVSp stop-loss frameshift: VEP 116.1 emits extTer, vepyr emits the 116.0 fsTer form

  biodatageeks/vepyr#50 · Filter by author sitekwb opened on Aug 25, 2026

• HGVS 3'-shift silently skipped when transcript has bam_edit_status='failed' (wrong HGVSc, empty HGVS_OFFSET, no error)

  bug
  biodatageeks/vepyr#32 · Filter by author sitekwb opened on Jul 13, 2026
  1

• CDS-terminus edge cases: Protein_position range truncated, insertion after last CDS base placed inside the CDS, spurious stop_retained_variant

  bug
  biodatageeks/vepyr#31 · Filter by author sitekwb opened on Jul 13, 2026
  1

• MotifFeature: Feature ID and MOTIF_NAME always empty, and overlapping motifs collapsed into one entry (accounts for 100% of the VEP-116 coverage gap)

  bug
  biodatageeks/vepyr#30 · Filter by author sitekwb opened on Jul 13, 2026
  1

• pick_order: a list is silently accepted and IGNORED (falls back to default order → 14.7% wrong --pick_allele output, no error)

  bug
  biodatageeks/vepyr#29 · Filter by author sitekwb opened on Jul 12, 2026
  1

• Defer HGVSc + output materialization until after pick (engine computes them for all overlapping transcripts pre-pick)

  biodatageeks/vepyr#18 · Filter by author mwiewior opened on Jun 15, 2026

• Integrate RefSeq and merged VEP cache flags

  biodatageeks/vepyr#10 · Filter by author mwiewior opened on Apr 10, 2026
  1

• Cap tokio blocking thread pool with max_blocking_threads(partitions)

  biodatageeks/vepyr#7 · Filter by author mwiewior opened on Apr 1, 2026