QTL-Portal: View & explore summary statistics in your browser

Getting Started

Prerequisites

• Docker

Installation

1. Clone this repo

   git clone https://github.com/atokolyi/qtl_portal.git

2. Start the QTL portal

   cd qtl_portal
   docker-compose up -d

3. Open the QTL portal in your web browser by visiting http://localhost:50580

Usage

Example using GTEX summary statistics

1. Download phenotype-level and nominal summary statistics

cd data
wget https://storage.googleapis.com/gtex_analysis_v8/single_tissue_qtl_data/GTEx_Analysis_v8_eQTL.tar
untar GTEx_Analysis_v8_eQTL.tar

2. Import summary statistics using the import-gtex helper script

• Import is of the format: id_name phenotype-summary-statistics.tsv nominal-summary-statistics.tsv

   docker exec -it qtl_portal-mysql-server-1 import-gtex GTEX-Lung-eQTLs \
      data/GTEx_Analysis_v8_eQTL/Lung.v8.egenes.txt.gz \
      data/GTEx_Analysis_v8_eQTL/Lung.v8.signif_variant_gene_pairs.txt.gz

2. View the imported summary statistics

Refresh the QTL Portal (http://localhost:50580) and click GTEX-Lung-eQTLs in the toolbar.

Formatting other summary statistics

1. Import summary statistics

• Copy summary statistics to data/
• Import is of the format: id_name display_name phenotype-summary-statistics.tsv nominal-summary-statistics.tsv

  docker exec -it qtl_portal-mysql-server-1 import eqtl eQTL data/phenotype-summary-statistics.tsv data/nominal-summary-statistics.tsv

• phenotype-summary-statistics.tsv is a tab-separated file with column names:
• nominal-summary-statistics.tsv is a tab-separated file with column names:

2. View the imported summary statistics

Refresh the QTL Portal (http://localhost:50580) and click the name in the toolbar

3. Delete imported summary statistics

• Summary statistics imported in to the database persist through reboots unless deleted with:

  docker exec -it qtl_portal-mysql-server-1 delete eqtl

License

Distributed under the GPLv3 License. See LICENSE.txt for more information.