broadinstitute/gtex-pipeline

Name: gtex-pipeline

Owner: Broad Institute

Description: GTEx Consortium data production and analysis pipelines

Created: 2016-02-11 13:53:46.0

Updated: 2018-01-04 06:55:28.0

Pushed: 2017-12-12 20:47:26.0

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Size: 110

Language: Python

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README

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.