megSAP
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a Medical Genetics Sequence Analysis Pipeline
- [x] fix bug in mapping pipeline: - [x] reads are lost during mapping - [x] determine step and fix - [ ] add check for sufficient file size/read count...
- [ ] allow reference base to be effect allele (required for some lifted SNPs) - [ ] adapt megSAP conversion script - [ ] adapt `VcfCalculatePRS` to handle this...
Dragen offers special callers for several medically relevant genes: https://developer.illumina.com/news-updates/dragen-4-2-enhanced-machine-learning-new-targeted-callers-and-more https://support-docs.illumina.com/SW/dragen_v42/Content/SW/DRAGEN/TargetedCalling.htm (enable with --enable-targeted=true) Especially relevant are: - SMN1/2
check if the following files exists for all LR samples - [ ] ROH - [ ] repeat expansions - [ ] methylation data (modkit) - [ ] CNVs -...
example: https://pubmed.ncbi.nlm.nih.gov/37081487/ [pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls]( https://pubmed.ncbi.nlm.nih.gov/37081487/)
- [ ] create `ngs-bits` tool - [ ] implement in `megSAP` pipeline - [ ] add filter in GSvar
Questions for meeting on Fr 28.07.23: howto configure SampleSheet to get: - [x] BAM, VCF small variant, VCF structural variants - [ ] benchmark with and without DRAGEN-ML (the on-site...