megSAP
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imgag
a Medical Genetics Sequence Analysis Pipeline
germline - rare disease ======================= - optimal cohort size - cohort selection - no relatives - only indices? - RNA QC - exons/genes that are lowly/not expressed - validation -...
bwa-mem2 does not work on newer AMD CPUs out of the box possble solutions: - limit to AVX2 - compile own version of bwa-mem2 [issue on Zen4](https://github.com/bwa-mem2/bwa-mem2/issues/236#issuecomment-1754209236)
Thanks to Elena for helping to collect these Issues. Some of these issues are cosmetic or readability improvements that might be hard to change in the database structure, so we...
- [ ] test mapping of cfDNA - [ ] check UMI support - [ ] test RNA mapping - [ ] implement in megSAP - [ ] implement in...
Snakemake code: https://github.com/imgag/megLR/blob/main/workflow/rules/cnv.smk - [x] implement
- [x] try calling with Varscan -> only calls the insertion but not the deletion.... - [x] dragen + evidence BAM -> not conclusive, only part of the region covered...
Add haplotype information to megSAP/GSvar. Should be easy for long-read - also possible for short-read? ToDos: - [ ] check for existing haplotype databases - [ ] check for existing...
Examples: - DX208004_01 chr13:32,911,530-32,911,900 - DX195929_01 chr2:25498395 - DX194025_01 chr13:48941612 - DNA2309843_02 chr7:5995692 (SVA insertion in PMS2) Tools: - MELT (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8934628/) Todo: - Check for other tools (MELT is slow...
ToDo: - [ ] configure one or several annotation sources in the megSAP INI: - VCF.GZ file - list of info entries - info prefix for output (optional) - list...