Published June 22, 2026 | Version 2026_06
Software Open

imgag/megSAP: 2026_06

Authors/Creators

  • 1. Institute of Medical Genetics and Applied Genomics
  • 2. Institut für Medizinische Genetik und Angewandte Genomik
  • 3. @MHH-Humangenetik
  • 4. PhD Student at Central Institute of Mental Health
  • 5. Boehringer Ingelheim
  • 6. Avera Cancer Institute
  • 7. Red Hat GmbH

Description

What's new

  • general changes:
    • updated tools and databases
    • processing system now also contains the sequencing platform: Illumina, ONT, PacBio
    • added analysis time logging for germline single sample, germline trio, somatic tumor-normal and somatic tumor-only
    • annotation changes:
      • added support for custom annotations from BED files (before only VCFs were possible as custom annotation source)
      • replaced SpliceAI default transcript definitions (they are from 2016), by transcript definitions based on Ensembl 115
      • about 30% speed-up of the annotation pipeline by removing VEP
      • made AlphaMissense optional because of license
  • short-read single-sample pipeline:
    • removed support for small variant caller `freebayes´
    • removed support for indel-realignment with ABRA2 (not needed anymore because DeepVariant does indel-realignment on the fly)
    • added support for DRAGEN 4.4 (now 4.3 and 4.4 are supported)
      • small variants: enabled mosaic calling
      • CNVs: enabled mosaic calling
      • enabled targeted callers, repeat expansion, HLA, VNTR, MRJD, PGX and star-allele calling
  • short read multi/trio pipeline:
    • gVCF merging was replaced by merging single sample VCF files
      • uncalled variants are checked in CRAM so that depth/allele frequency are available in the VCF/GSvar file for all samples
      • genotypes of uncalled variants are corrected if allele frequency is larger than 10% (het) or 90% (hom)
  • long-read single-sample pipeline:
    • partly methylated reads are now supported (needed for PacBio)
    • small variants: added mosaic calling for ONT samples with super-accuracy base calling
    • REs: added column with insertion calls at repeat loci allow recovering missed RE calls
    • updates and refactoring of methylation calling
      • added methylation plots with background cohort for each imprinting site
  • long-read multi/trio pipeline:
    • implemented preliminary version of PacBio multi-sample calling
    • gVCF merging was replaced by merging single sample VCF files
      • uncalled variants are checked in CRAM so that depth/allele frequency are available in the VCF/GSvar file for all samples
      • genotypes of uncalled variants are corrected if allele frequency is larger than 10% (het) or 90% (hom)
  • short-read tumor-normal pipeline:
    • speed up annotation of RNA depth and AF
    • activated DRAGEN SV calling
    • added support for DeepSomatic as small variant caller (the default caller is still strelka2)
  • short-read tumor-only pipeline:
    • added NGSD import of somatic CNVs and SVs
    • added NGSD import of QC data
    • added support for DeepSomatic as small variant caller (the default caller is still VarScan2)

Full Changelog: https://github.com/imgag/megSAP/compare/2025_10...2026_06

Files

imgag/megSAP-2026_06.zip

Files (394.0 MB)

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md5:f21570ff5511610ae97adf9a4af2e63c
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Additional details

Related works

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

Software

Repository URL
https://github.com/imgag/megSAP