Issues

• Port read orientation filtering from GATK

  broadinstitute/permutect#343 · Filter by author davidbenjamin opened on Nov 11, 2026

• Feature clustering model density don't line up well with data

  broadinstitute/permutect#335 · Filter by author davidbenjamin opened on Nov 4, 2026

• Assuming independent reads in feature clustering isn't really true

  broadinstitute/permutect#334 · Filter by author davidbenjamin opened on Nov 4, 2026

• Consider concatenating variant-level tensor and haplotype embeddings after the gated MLP

  broadinstitute/permutect#332 · Filter by author davidbenjamin opened on Nov 4, 2026

• Statistical test for rejecting low-AF cluster

  broadinstitute/permutect#324 · Filter by author davidbenjamin opened on Nov 3, 2026

• GATK Bug in Permutect read features

  broadinstitute/permutect#322 · Filter by author davidbenjamin opened on Nov 2, 2026

• Polymerase slippage model

  broadinstitute/permutect#320 · Filter by author davidbenjamin opened on Oct 30, 2026
  

• How does Permutect avoid filtering real mutations that resemble artifacts?

  broadinstitute/permutect#296 · Filter by author nh13 opened on Aug 4, 2026

• TENT – adaptation on unlabeled target data by minimizing entropy

  broadinstitute/permutect#248 · Filter by author davidbenjamin opened on Dec 12, 2025

• Artifact AF spectrum in the artifact model

  broadinstitute/permutect#245 · Filter by author davidbenjamin opened on Dec 12, 2025