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.