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Zenodo
2025
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| Online-Zugang: | https://doi.org/10.5281/zenodo.15116291 |
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- # Analysis pipelines for the [GTEx Consortium](https://www.gtexportal.org) and [TOPMed](https://www.nhlbi.nih.gov/science/trans-omics-precision-medicine-topmed-program) 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](https://github.com/broadinstitute/wdl). The pipelines are available on [FireCloud](http://firecloud.org), 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](https://github.com/broadinstitute/gtex-pipeline/blob/master/TOPMed_RNAseq_pipeline.md).