2025_10

What's new

• General changes
  • Updated databases and several tools
    • Note that way more transcripts are contained in Ensembl 115. See https://www.ensembl.info/2025/02/14/cool-stuff-ensembl-vep-can-do-reduce-the-number-of-human-transcripts-you-need-to-consider-without-missing-results/ and https://www.ensembl.info/2025/09/02/ensembl-115-has-been-released/.
  • added support for singularity in addition to apptainer
  • updated OS in tool containers to Ubuntu 24.04
  • Illumina DRAGEN
    • simpifiled file handling: renaming files is not longer necessary. Just copy the DRAGEN output into the dragen sub-folder of a processed sample folder.
    • added multi-version installation support by specifying the DRAGEN version in the megSAP settings. Note: only DRAGEN 4.3 is supported right now.
    • removed settings parameter 'use_dragen_sv_calling': Using DRAGEN SV files when they are available because they are way better than Manta (see performance page).
    • added support for ORA as input for DRAGEN
  • ensure consistent fallback to data_folder when local_data copy is missing/incomplete
• germline WES/WGS:
  • DeepVariant is now the default caller for small variants (was freebayes before)
• germline lrGS:
  • added Clair3 GPU support
  • updated Straglr to version 1.5.4
  • improved PacBio support
• germline RNA:
  • updated arriba to version 2.5.1
• somatic tumor-only:
  • renamed the pipeline script to somatic_tumor_only.php
  • improved sensitivity for low AF variants and runtime
• somatic tumor-normal:
  • renamed the pipeline script to somatic_tumor_normal.php
  • added support for WGS

Full Changelog: 2025_03...2025_10

2025_03

What's Changed

• General changes
  • All tools are containerized now using Apptainer
  • Cleanup of repository (removed unused scripts, script sub-folder structure)
  • improved PHP8 support
• germline lrGS:
  • added CRAM support
  • added Methylartist plots
  • improved ROH detetcion by exclude regions and adapted parameters
  • many small changes and bugfixes
• germline WES/WGS:
  • added option to call small variants with DeepVariant
  • improved SV handling: INV conversion, and removal of duplicate variants
  • improved ROH detetcion by exclude regions
  • added support for NovaSeqX+ software version 1.3 and Illumina Dragen 4.3
  • many small changes and bugfixes
• somatic tumor-only:
  • added import of tumor-only variants into NGSD
  • added annotation of tumor-only variant counts in VCF/GSvar

Full Changelog: 2024_09...2025_03

2024_09

Most important changes:

• first production version of long-read pipeline (ONT)
• updated tools and databases of all pipelines
• added support partial data analysis on Nova Seq X Plus
• improved PRS calculation (imputed variants, etc)
• added optional RefSeq annotation (see settings documentation).
• added optional custom annotations in GSvar/VCF from VCFs (see settings documentation).

2023_11

Most important changes:

• added AlphaMissense (removed Sift and PolyPhen)
• switched from BAM to CRAM
• MaxEntScan: added acceptor/donor gain predictions (based on own implementation of MaxEntScan)
• Improved DRAGEN support (MappingQC now does ReadQC, gVCF, ...)
• improved long-read pipeline
• added tumor-normal calling based on DRAGEN (optional)
• switched to SpliceAI raw scores

2023_04

Changes of 2023_04 release:

• updated tools and databases
• fixed false duplications in GRCh38 (see details).
• germline DNA pipeline: Improved sensitivity of non-diploid variant calling (mitochondrial, mosaic).
• germline DNA pipeline: Added calling of mitochondrial variants for shallow WGS analysis.
• germline DNA pipeline: Added small variant and structural variant calling on Dragen when '-use_dragen' is enabled (see details).
• using VcfAnnotateConsequence as primary source for consequence annotations of small variants now instead of VEP.
• gnomAD exome data from VEP is no longer used. Only gnomAD genome data is used now for variant with AC>=1000.
• minor fixes and updates.

2022_08

Second release for hg38:

• update tools and databases
• added RNA pipeline
• minor other changes

2021_12

First version based on GRCh38 genome build

0.2

Release 0.2

This is the 2019 stable version of megSAP.
Use this release if you want to install megSAP.