NON_CODING PathogenicityFilter

[julesjacobsen]

15.1.0 2026-06-09

• The pathogenicityFilter now has a target option to specify whether to filter non-coding variants. The default is
  ALL but NON_CODING can be specified to filter non-coding variants. This change only affects variants found in
  non-coding regions. We recommend using the standard pathogenicityFilter{keepNonPathogenic: true} for exome analysis,
  but when running genomiser (i.e. including REMM/CADD/SPLICE_AI and all non-coding regions) or any analysis including
  non-coding regions, use pathogenicityFilter{keepNonPathogenic: false, target: NON_CODING}. See the documentation
  for more details.

Updated examples/preset-genome-analysis.yml to use new defaults. UPDATE YOUR SCRIPTS TO USE THESE FOR IMPROVED ACCURACY.

• Fix for issue #629 - replace commas in disease names with semicolons.
• Fix for issue #633 - calculate variant score for non-symbolic insertions > 1kb.
• Change for issue #635 - Display CADD phred scores alongside the scaled scores in HTML.

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This discussion was created from the release NON_CODING PathogenicityFilter.