megSAP
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imgag
a Medical Genetics Sequence Analysis Pipeline
Add a different cfDNA type: fixed set of monitoring variants, which defined in ProcessingSystem, but performs targeted calling
- [ ] benchmark FANSe (Towards an accurate and robust analysis pipeline for somatic mutation calling // Gong Zhang, Jingjie Jin, Zixi Chen, Jinchao Liu and Hongli Du) - [...
- [ ] add imprinting track to IGV - [ ] calculate from in-house db - [ ] add significant ASE to circos plot - [ ] cutoffs?
- Snakemake code: https://github.com/imgag/megLR/blob/main/workflow/rules/variant_calling.smk - Problem: PepperMarging needs GPU acceleration --> can only run on SRV019 - modular approach? (queue each step separatly to SGE) - [x] decide which variant...
- project folder: W:\projects\research\21073N_SEQ418081722_trio - sample: 21073LRa015: HG002 - [ ] validate CNVs against GIAB reference - [ ] repeat validation as soon as deeper samples are available (60x)
hla-genotyper will be benchmarked and compared to OptiType. If successful, we need to caclulate the HLA genotypes for our somatic cohort and we will compare it to the european distribution...
-Annotate counts based on disease group like for small variants - Annotate same variants with class 4/5 > Add KEEP filter for those.
:eyes: Some source code analysis tools can help to find opportunities for improving software components. :thought_balloon: I propose to [increase the usage of combined operators](https://www.php.net/manual/en/language.operators.assignment.php#language.operators.assignment.arithmetic "Description for assignment operators") accordingly....
- gene definition as overlap of ensembl transcripts - flag partially affected genes - implement also for structural variants (DEL, INV and DUP)