Quick start

Customize pipelines

Before running any of the snakefiles, you may want to adjust the number of threads used by different steps in the pipeline. To do this, modify the threads: property of a given rule.

If you are running on a computing cluster, you will need a profile and may need to add resources: directives to the snakefiles.

Run the preprocessing pipeline on your VCF files

Instructions here

Annotate variants

Instructions here

Example DeepRVAT runs

In each case, replace [path_to_deeprvat] with the path to your clone of the repository.

Note that the example data used here is randomly generated, and so is only suited for testing whether the deeprvat package has been correctly installed.

Run the association testing pipeline with pretrained models

DEEPRVAT_REPO_PATH="[path_to_deeprvat]"
mkdir deeprvat_associate
cd deeprvat_associate
ln -s "$DEEPRVAT_REPO_PATH"/example/* .
ln -s "$DEEPRVAT_REPO_PATH"/pretrained_models
ln -s config/deeprvat_input_pretrained_models_config.yaml . # Get the corresponding config.
snakemake -j 1 --snakefile "$DEEPRVAT_REPO_PATH"/pipelines/association_testing_pretrained.snakefile

Run association testing using REGENIE on precomputed burdens

mkdir deeprvat_associate_regenie
cd deeprvat_associate_regenie
ln -s [path_to_deeprvat]/example/* .
ln -s precomputed_burdens/burdens.zarr .
snakemake -j 1 --snakefile [path_to_deeprvat]/pipelines/association_testing_pretrained_regenie.snakefile

Run the training pipeline on some example data

DEEPRVAT_REPO_PATH="[path_to_deeprvat]"
mkdir deeprvat_train
cd deeprvat_train
ln -s "$DEEPRVAT_REPO_PATH"/example/* .
ln -s config/deeprvat_input_training_config.yaml . #get the corresponding config.
snakemake -j 1 --snakefile "$DEEPRVAT_REPO_PATH"/pipelines/run_training.snakefile

Run the full training and association testing pipeline on some example data

DEEPRVAT_REPO_PATH="[path_to_deeprvat]"
mkdir deeprvat_train_associate
cd deeprvat_train_associate
ln -s "$DEEPRVAT_REPO_PATH"/example/* .
ln -s config/deeprvat_input_config.yaml .
snakemake -j 1 --snakefile "$DEEPRVAT_REPO_PATH"/pipelines/training_association_testing.snakefile