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MetaRNN for pathogenicity prediction of nsSNVs and nfINDELs

Quick start guide

  1. Download file package (file size: 13G):

    wget -c https://usf.box.com/shared/static/c4656df0rz10vw6z7ra11mkw69ulr9d3 -O MetaRNN.tar.gz

    OR open the save link in any web browser: https://usf.box.com/shared/static/c4656df0rz10vw6z7ra11mkw69ulr9d3

    OR get it from figshare.

  2. Extract downloaded folder:

    tar -xf MetaRNN.tar.gz
cd MetaRNN

  3. Create conda environment with required packages and activate the virtual environment:

    conda env create -f environment.yml
conda activate MetaRNN

  4. Run example VCF file in hg38 genome assembly:

    python ./MetaRNN.py hg38 test.vcf

Notes

  • Supplementary Tables and model analyses associated with the publication are available under folders Data and Notebooks.

  • Tensorflow models of MetaRNN and MetaRNN-indel are available under Resources/Models, with names RNN_DNN_adam.h5 and RNN_DNN_indel_adam.h5, respectively.

  • The code for the MetaRNN pipeline, including data preparation and making predictions, is available under Resources/Pipeline.

metarnn's People

Contributors

chang-li2019 avatar

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