Various scripts and pipelines developed for Genes & Health as part of the BRaVa consortium.
In brief, the following work is undertaken:
- Phasing of Genes & Health. This is performed using Shapeit5, following Lassen et al. (2023).
- Variant annotation and encoding of additive/recessive genotypes. This is in accordance with call_chets. Annotation follows the BRaVa guidelines.
- Testing for recessive effects. Future work
- In
recessive_encoding/run_call_chets.sh, thecpp_dir/get_non_ref_sitesdoes almost the same as the proceeding line with bcftools, but the latter is safer to use and probably faster. - Occasionally, I've noted that some parts of the recessive encoding pipeline crash, giving an something crashes occasionally with throwing an "OSError: [Errno 12] Cannot allocate memory". Can't find why this happens, but re-running the corresponding task solves the problem.