Benedikt Schnur

GSVar: Make `KeepFastq` of NovaSeqX SampleSheet export configurable in settings

1

We only archive BAM/CRAM files thus we do not need intermediate FastQs. Please make this option configurable to save some precious disk space. 😉 https://github.com/imgag/ngs-bits/blob/554919ea577fa225a05c815bc0bf567909f66927/src/cppNGSD/NGSD.cpp#L5644

I get the following error after running `apptainer exec --pwd /megSAP/data -B XXX:/megSAP/data/data_folder/ XXX/megSAP_master.sif ./download_dbs.sh`: ``` zcat CADD_InDels_1.7_GRCh38.tsv.gz | php $src/Install/db_converter_cadd.php -build GRCh38 -in - -out - | apptainer exec...

Calls to DB dependent tool when running without db

2

At https://github.com/imgag/megSAP/blob/a29981c561e27c9b4dc5a60bf95955d129235122/src/Pipelines/analyze.php#L735 and https://github.com/imgag/megSAP/blob/a29981c561e27c9b4dc5a60bf95955d129235122/src/Pipelines/analyze.php#L747 `BedAnnotateGenes` is called without checking for DB availability which is usually done in other places: https://github.com/imgag/megSAP/blob/a29981c561e27c9b4dc5a60bf95955d129235122/src/Pipelines/analyze.php#L249

On our NovaSeqX the column `BedFile` in the `[DragenEnrichment_Data]` section needs to be prepended by `DragenEnrichment/` (so i.e. `DragenEnrichment/lotusv2.bed`) for the DRAGEN pipeline to work. https://github.com/imgag/ngs-bits/blob/0d75af002bd019299aa771ccdcfc8ce2eacb1f9e/src/cppNGSD/NGSD.cpp#L6031

GSVar: Extend variant classification

1

We need to add additional (sub)information to the current classification system such as `R` for risk-allele or `m` for moderate/low penetrance variants.

Complex structural variant visualization: https://github.com/PacificBiosciences/SVTopo Ist von PacBio, aber ich wüsste nicht, warum das nicht generell funktionieren sollte. Zugehöriges Paper: https://doi.org/10.1186/s12864-025-12088-6

LongReads: Header information discrepancy

1

For germline analysis, VCF header information is added in `analyze.php` directly. For the longread pipeline, it is not handled in `analyze_longread.php` but downstream in `vc_clair.php`. This leads to `vc_deepvariant.php` not...