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.