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