Center for Statistical Genetics

pheweb

A tool to build a website to browse hundreds or thousands of GWAS.

locuszoom

A Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources.

Minimac4

libStatGen

Useful set of classes for creating statistical genetic programs.

savvy

Interface to various variant calling formats.

topmed_variant_calling

LDServer

Fast API server for calculating linkage disequilibrium

encore

Encore Analysis Server

localzoom

Make interactive LocusZoom plots from a local GWAS file

raremetal

A flexible tool for meta-analysis

ruth

Robust Unified Hardy-Weinberg Equilibrium Test

imputationserver

TOPMED Imputation Server: A new web-based service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity

encore-client-r

An R package to interact with the Encore analysis server

hds-util

bravo_api

Server side data processing and retrieval endpoints for BRAVO

locuszoom-hosted

A web service to upload and share GWAS results with LocusZoom.js

bravo-infrastructure

Provisioning and deployment of example BRAVO vignette.

bravo_data_prep

Work flows and tools to create data that backs the BRAVO API.

bravo_vue

BRAVO's Vue JS based UI.

terraform-aws-imputation-server

A set of Terraform Modules for deploying an imputation server on AWS

terraform-bravo-slurm

Infrastructure for slurm on GCP to provide compute for Bravo data prep

ansible-bravo-deploy

Anisble deployment roles and playbook for BRAVO API and UI

ansible-bravo-slurm

Deployment of data and tooling to run BRAVO data prep on a GCP slurm.

bravo_ui

Front end to navigate and visualize results from BRAVO API

cloudgene

A framework to build Software As A Service (SaaS) platforms for data analysis pipelines.

di2hap

A tool for converting diploid geontypes to haploid.

rand-recom

Tool for randomly applying artificial recombination

telomere-length-pipeline

A cloud-based pipeline to estimate telomere lengths from WGS data using Telseq

topmed-methylation-qtl

PIpeline for TOPMed methylation QTL analysis.

vuptool

Tool for detecting and handling genomic variant under methylation probes