Analysis pipelines for the GTEx Consortium and TOPMed

This repository contains analysis pipelines for:

• RNA-seq alignment, quantification, and quality control
• eQTL mapping and annotation
• Allele-specific expression quantification
• Generation of the collapsed annotation used for gene-level expression quantification

Pipeline components are available as docker images, and execution scripts are provided in WDL. The pipelines are available on FireCloud, in the namespace broadinstitute_gtex. All Python scripts are written in Python 3.

A detailed description of the RNA-seq pipeline settings used for TOPMed is provided in TOPMed_RNAseq_pipeline.md.