Published June 15, 2026 | Version 2026_06
Software Open

imgag/ngs-bits: 2026_06

Authors/Creators

  • 1. Institute of Medical Genetics and Applied Genomics
  • 2. Institut für Medizinische Genetik und Angewandte Genomik
  • 3. University of Tübingen
  • 4. @MHH-Humangenetik
  • 5. Avera Cancer Institute

Description

Changes:

  • removed Qt5 support
  • added tools: NGSDExportSpliceAI, NGSDImportCSpec, NGSDTransferReportConfig, SampleIdentity, TranscriptToProtein, TsvAnnotate, TsvTo, VcfAnnotateFrequency, VcfMerge
  • BedAnnotateFreq: changed default for -min_mapq from 1 to 20
  • BedIntersect: added parameter -annotation
  • NGSDExportGenes: added gnomAD pli column
  • NGSDExportAnnotationData: Gene info entries now contains only keys with a value
  • TrioMendelianErrors: added parameter -dot_as_wt
  • UpdHunter: added parameter -var_use_special_calls and fixed bug in handling of exclude regions.
  • VcfAnnotateFromBed: added parameter -desc
  • VcfFilter: added parameters -info_flags and -info_flags_exclude
  • NGSD changes:
    • added table user_action_permissions for action permissions of restricteed users in GSvar
    • added table analysis_time for tracking analysis times of megSAP analyses
    • added table report_configuration_failed_transfer for manually fixing report configs that could not be transferred from one sample to another automaticalls
    • added table db_import_info to track version/date of database imports into NGSD
    • added table cspec_data for gene-specific guidelines for variant interpretation
    • table geneinfo_germline: added field gnomad_pli
    • table somatic_cnv_callset: made field ps_normal_id nullable to allow import of tumor-only variants
    • table somatic_snv_callset: made field processed_sample_id_normal nullable to allow import of tumor-only variants
    • table repeat_expansion: added field min_pathogenic_hom to allow lower cutoff if the repeat expansion is homozygous

Full Changelog at: https://github.com/imgag/ngs-bits/compare/2025_12...2026_06

Note: Please do not use the auto-generated 'Source code' packages - they will not work!

Files

imgag/ngs-bits-2026_06.zip

Files (260.9 MB)

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Additional details

Related works

Is supplement to
Software: https://github.com/imgag/ngs-bits/tree/2026_06 (URL)

Software

Repository URL
https://github.com/imgag/ngs-bits