Broad Institute

gatk

Official code repository for GATK versions 4 and up

cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

gtex-pipeline

GTEx & TOPMed data production and analysis pipelines

warp

WDL Analysis Research Pipelines

seqr

web-based analysis tool for rare disease genomics

gatk-sv

A structural variation pipeline for short-read sequencing

depmap_omics

What you need to process the Quarterly DepMap-Omics releases from Terra

gnomad-browser

Explore gnomAD datasets on the web

sam

workbench identity and access management

pyqtl

Collection of analysis tools for quantitative trait loci

firecloud-orchestration

rawls

Rawls service for DSDE

covid19-testing

COVID-19 Diagnostic Processing Dashboard

firecloud-ui

FireCloud user interface for web browsers.

palantir-workflows

Utility workflows for the DSP hydro.gen team (formerly palantir)

molecular-data-provider

Molecular Data Provider

warp-tools

This repository contains all containers that WARP uses.

ddp-study-server

Pepper Study Server

workbench-libs

Workbench utility libraries

dsp-appsec-infrastructure-apps

This repository hosts DSP AppSec internal infrastructure apps deployed in GKE.

TAG-public

Official workflows published by the Broad Institute's Genomics Platform Translation Analysis Group (TAG)

tgg_methods

Repo for miscellaneous methods developed by the methods group that don't fit anywhere else

azure-warp-joint-calling

Exploration of Joint Calling Exomes with Cromwell on Azure using WARP Joint Calling Pipeline

cromwhelm

Tentative first steps into the world of helm charts

ddp-angular

Angular code for participant-facing pepper studies

dig-aggregator-methods

Monorepo of methods implemented for the Aggregator

dig-loam

Pipelines encoded in .loam files

genetics-kp-dev

GPP-bulk-rnaseq-protocols

Bulk RNA sequencing protocols used at the Broad Genetic Perturbation Platform

position-effect-correction