Marc Sturm

@egor-dolzhenko Sorry, we don't have WGS data from positive controls since no genome will be done when the repeat is tested positive.

I think the reason is that the libAbra.so is missing in the jar file. It was there in v 2.23.

Papers: - [Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing - Nature Biotechnology](https://www.nature.com/articles/s41587-021-00994-5) - [Establishing community reference samples, data and call sets for benchmarking cancer mutation...

Implemented tool to fix BAMs that were mapped with a hg38 genome without masked false duplications: https://github.com/imgag/megSAP/blob/master/src/Tools/bam_fix_unmasked_duplications.php

The legacy version 1,0.3 works as I said above. Version 1.0.10 still does not work. `vcfwave --quiet` no longer crashes, but does not decompose the MNP: ``` ##fileformat=VCFv4.2 ##fileDate=20231214 ##source=freeBayes...

@c-schroeder Axel wird das implementieren, sobald du bestätigt hast dass die Implementierung so ok wäre

Implement RE calling for long-reads - [x] check for available tools (STRling, ...) - [ ] benchmark tools by coparing to short-read GS - [ ] validate postive controls