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# AbExp variant effect prediction pipeline
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AbExp is a tool to predict aberrant gene underexpression in 48 human tissue based on DNA sequence variants.
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AbExp is a tool to predict aberrant gene expression in 49 human tissue based on DNA sequence variants.
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It was trained on aberrant gene expression calls from the GTEx dataset.
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This repository contains a bioinformatics software pipeline for calculating **AbExp variant effect predictions**, taking vcf files as input.
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## Setup
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1) install conda and mamba on your system
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1) install conda and mamba on your system.
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Tip: Use the [conda-libmamba-solver](https://conda.github.io/conda-libmamba-solver/user-guide/) for an improved experience when installing environments with `conda`!
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2) To download the VEP cache (if not existing yet):
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```bash
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VEP_CACHE_PATH="<your cache path here>"

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