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ignores python notebook links for linting
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tkmamidi committed Jan 26, 2024
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Showing 1 changed file with 6 additions and 3 deletions.
9 changes: 6 additions & 3 deletions docs/build_DITTO.md
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Expand Up @@ -86,9 +86,11 @@ python src/annotation_parsing/parse_single_sample.py -i clinvar.vcf.gz.variant.c
-o clinvar.vcf.gz.variant.csv_parsed.csv.gz -c configs/opencravat_train_config.json
```

<!-- markdown-link-check-disable -->
Filter and process the annotations as shown in this [python
notebook](src/annotation_parsing/opencravat_clinvar_filtering_80-20-20.ipynb). This will output training and testing
notebook](../src/annotation_parsing/opencravat_clinvar_filtering_80-20-20.ipynb). This will output training and testing
data to train the neural network.
<!-- markdown-link-check-enable -->

## Tune and Train DITTO

Expand Down Expand Up @@ -117,6 +119,7 @@ Follow the below steps to install and add more databases for annotation and befo
4. Follow the steps from Preprocessing above to parse, filter, process, tune and train DITTO.

## Benchmarking

Please follow the [python notebook](../../src/analysis/opencravat_latest_benchmarking-Consequence_80_20.ipynb) to benchmark
<!-- markdown-link-check-disable -->
Please follow the [python notebook](../src/analysis/opencravat_latest_benchmarking-Consequence_80_20.ipynb) to benchmark
DITTO with other pathogenicity predition tools. It also has code snippets to generate testing metrics and SHAP plots.
<!-- markdown-link-check-enable -->

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