zerland / gtex-v8

Notebooks and scripts for reproducing analyses and figures from the V8 GTEx Consortium paper

GTEx V8

This repository contains notebooks and scripts for reproducing analyses and figures from the paper The GTEx Consortium atlas of genetic regulatory effects across human tissues, Science, 2020.

Requirements

The following Python modules are needed to run the notebooks: numpy, pandas, scipy, ipython, jupyter, matplotlib, seaborn, qtl

The notebooks require data from the GTEx Portal to run (by default, the data is assumed to be accessible in the data directory of this repository). Running the following commands will download the relevant files:

cd data

# QTLs
wget https://storage.googleapis.com/gtex_analysis_v8/single_tissue_qtl_data/GTEx_Analysis_v8_eQTL.tar && \
    tar xf GTEx_Analysis_v8_eQTL.tar && rm GTEx_Analysis_v8_eQTL.tar

wget https://storage.googleapis.com/gtex_analysis_v8/single_tissue_qtl_data/GTEx_Analysis_v8_sQTL.tar && \
    tar xf GTEx_Analysis_v8_sQTL.tar && rm GTEx_Analysis_v8_sQTL.tar

wget https://storage.googleapis.com/gtex_analysis_v8/single_tissue_qtl_data/GTEx_Analysis_v8_eQTL_independent.tar && \
    tar xf GTEx_Analysis_v8_eQTL_independent.tar && rm GTEx_Analysis_v8_eQTL_independent.tar

wget https://storage.googleapis.com/gtex_analysis_v8/single_tissue_qtl_data/GTEx_Analysis_v8_sQTL_independent.tar && \
    tar xf GTEx_Analysis_v8_sQTL_independent.tar && rm GTEx_Analysis_v8_sQTL_independent.tar

wget https://storage.googleapis.com/gtex_analysis_v8/single_tissue_qtl_data/GTEx_Analysis_v8_trans_eGenes_fdr05.txt

wget https://storage.googleapis.com/gtex_analysis_v8/single_tissue_qtl_data/GTEx_Analysis_v8_trans_sGenes_fdr05.txt

wget https://storage.googleapis.com/gtex_analysis_v8/single_tissue_qtl_data/GTEx_Analysis_v8_eQTL_expression_matrices.tar && \
    tar xf GTEx_Analysis_v8_eQTL_expression_matrices.tar && rm GTEx_Analysis_v8_eQTL_expression_matrices.tar

wget https://storage.googleapis.com/gtex_analysis_v8/single_tissue_qtl_data/GTEx_Analysis_v8_eQTL_covariates.tar.gz && \
    tar xf GTEx_Analysis_v8_eQTL_covariates.tar.gz && rm GTEx_Analysis_v8_eQTL_covariates.tar.gz

wget https://storage.googleapis.com/gtex_analysis_v8/single_tissue_qtl_data/GTEx_Analysis_v8_sQTL_groups.tar.gz && \
    tar xf GTEx_Analysis_v8_sQTL_groups.tar.gz && rm GTEx_Analysis_v8_sQTL_groups.tar.gz

# fine mapping results
wget https://storage.googleapis.com/gtex_analysis_v8/single_tissue_qtl_data/GTEx_v8_finemapping_CAVIAR.tar && \
    tar xf GTEx_v8_finemapping_CAVIAR.tar && rm GTEx_v8_finemapping_CAVIAR.tar
wget https://storage.googleapis.com/gtex_analysis_v8/single_tissue_qtl_data/GTEx_v8_finemapping_CaVEMaN.tar && \
    tar xf GTEx_v8_finemapping_CaVEMaN.tar && rm GTEx_v8_finemapping_CaVEMaN.tar
wget https://storage.googleapis.com/gtex_analysis_v8/single_tissue_qtl_data/GTEx_v8_finemapping_DAPG.tar && \
    tar xf GTEx_v8_finemapping_DAPG.tar && rm GTEx_v8_finemapping_DAPG.tar

# annotation
wget https://storage.googleapis.com/gtex_analysis_v8/reference/gencode.v26.GRCh38.genes.gtf
wget https://storage.googleapis.com/gtex_analysis_v8/reference/WGS_Feature_overlap_collapsed_VEP_short_4torus.MAF01.txt.gz

A subset of the figures require genotype information. The VCF can be obtained from dbGaP (accession phs000424) or from AnVIL (requires dbGaP authentication).