Issues

• prioritization env: move blast/perl off 2015-era pins so Python and OpenSSL can be patched

  chore
  ylab-hi/ScanNeo2#232 · Filter by author riasc opened on Sep 30, 2026

• variants.py: allele matching can miss one ALT of a multiallelic MNP

  bug
  ylab-hi/ScanNeo2#225 · Filter by author riasc opened on Sep 29, 2026

• Unknown-residue (X) handling in variants.py: coarse skips, first-X-only trim, and frameshifts lost to a leading X in DownstreamProtein

  bug
  ylab-hi/ScanNeo2#223 · Filter by author riasc opened on Sep 28, 2026

• Mutect2 MIXED records (multiallelic SNV + indel) are dropped by SNV/indel selection

  bug
  ylab-hi/ScanNeo2#222 · Filter by author riasc opened on Sep 28, 2026

• Feature: Annotate neoantigen candidates with HLA loss and antigen-presentation defects

  ylab-hi/ScanNeo2#215 · Filter by author riasc opened on Sep 27, 2026

• Altsplicing events lose their transcript context and are re-fanned across all transcripts of the gene

  enhancement
  ylab-hi/ScanNeo2#210 · Filter by author riasc opened on Sep 26, 2026

• Neoepitope candidates carry no isoform-level expression evidence (quantification is gene-level)

  enhancement
  ylab-hi/ScanNeo2#209 · Filter by author riasc opened on Sep 26, 2026

• Prediction batches are sized by sequence count, but cost scales with residues

  enhancement
  ylab-hi/ScanNeo2#203 · Filter by author riasc opened on Sep 24, 2026
  2

• RNA variant calling reuses the DNA workflow (no SplitNCigarReads / splice-aware handling) → ~10–100× artifact inflation

  enhancement
  ylab-hi/ScanNeo2#192 · Filter by author riasc opened on Sep 21, 2026

• RNA editing neoepitopes: dedicated RNA-vs-DNA editing caller (CADRES-informed)

  enhancement
  ylab-hi/ScanNeo2#189 · Filter by author riasc opened on Sep 20, 2026

• RNA neoantigen filtering: separate self from tumor-specific (point mutations + A-to-I editing)

  enhancement
  ylab-hi/ScanNeo2#186 · Filter by author riasc opened on Sep 20, 2026
  2

• Extend matched-normal subtraction to the transcriptomic neoepitope sources

  enhancement
  ylab-hi/ScanNeo2#184 · Filter by author riasc opened on Sep 19, 2026

• Design: method-agnostic neoepitope output schema (report the metric, not the tool)

  ylab-hi/ScanNeo2#181 · Filter by author riasc opened on Sep 18, 2026

• MHC-II is effectively DR-only: DQ/DP alleles typed by HLA-HD are dropped downstream

  ylab-hi/ScanNeo2#180 · Filter by author riasc opened on Sep 17, 2026
  1

• Mutect2: GATK best-practice germline/artifact filtering (gnomAD + PON + contamination)

  ylab-hi/ScanNeo2#173 · Filter by author riasc opened on Sep 17, 2026

• Convert single-command samtools shell rules to v4.0.0/bio/samtools/* wrappers (deferred low-priority)

  chore
  ylab-hi/ScanNeo2#133 · Filter by author riasc opened on May 25, 2026

• Modernize the remaining Snakemake wrappers (tool-version-changing bumps)

  chore
  ylab-hi/ScanNeo2#104 · Filter by author riasc opened on May 20, 2026

• Annotate neoepitopes with cancer cell fraction (CCF) / clonality

  enhancement
  ylab-hi/ScanNeo2#95 · Filter by author riasc opened on May 20, 2026

• Add HERV as (potential) new source of neoantigens

  Feature

  ylab-hi/ScanNeo2#47 · Filter by author riasc opened on Mar 27, 2025