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Cleanup repo #66

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merged 4 commits into from
Apr 16, 2024
Merged

Cleanup repo #66

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c226b4c
Remove unused stuff
endast Apr 9, 2024
8fa7a39
Delete make_unrelated_cv_splits.R
endast Apr 15, 2024
e859885
Remove lsf references
endast Apr 15, 2024
e9654bc
Delete TODOS.md
endast Apr 15, 2024
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114 changes: 0 additions & 114 deletions TODOS.md
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211 changes: 0 additions & 211 deletions deeprvat/deeprvat/association_testing_pretrained.snakefile
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48 changes: 0 additions & 48 deletions deeprvat/seed_gene_discovery/lsf.yaml
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2 changes: 1 addition & 1 deletion docs/seed_gene_discovery.md
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This pipeline discovers *seed genes* for DeepRVAT training. The pipeline runs SKAT and burden tests for missense and pLOF variants, weighting variants with Beta(MAF,1,25). To run the tests, we use the `Scoretest` from the [SEAK](https://github.com/HealthML/seak) package (has to be installed from github).

To run the pipeline, an experiment directory with the `config.yaml` has to be created. An `lsf.yaml` file specifiying the compute resources for each rule in `seed_gene_discovery.snakefile` might also be needed depending on your system (see as an example the `lsf.yaml` file in this directory).
To run the pipeline, an experiment directory with the `config.yaml` has to be created.

## Input data

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