populationgenomics Goto Github PK

airtable-automation

alphafold-viewer

Viewer for AlphaFold

analysis-runner

ancestry

automated-interpretation-pipeline

Rare Disease variant prioritisation MVP

cellregmap-pipeline

WDL workflow to facilitate running CellRegMap

clinvarbitration

A side-project from the AIP, containing the code, logic, and documentation for the ClinVar consequence reassessment process in use at the CPG

cpg-additional-findings

cpg-cost-control

A Cloud Function to handle GCP billing budget notifications.

cpg-infrastructure

This repository is used to manage the infrastructure at the CPG

cpg-methods

Methods developed by the Centre for Population Genomics

cpg-python-template-repo

A template repository for python code, implementing the CPG setup guidelines

cpg-utils

Library of convenience functions specific to the CPG

cpgr

Centre for Population Genomics R utils and RMarkdown notebook templates

cromwell-kccg-mutect2-chip

Detect clonal haematopoiesis of indeterminate potential (CHIP) mutations using the GATK4 Mutect2 somatic variant calling pipeline and the Cromwell workflow engine.

cuking

CUDA-based KING relatedness estimation

dragmap

DRAGEN open-source mapper

exome-results-browsers

Results browsers for case-control studies of psychiatric diseases done at the Broad Institute

fewgenomes

CPG test dataset

gatk

Official code repository for GATK versions 4 and up

gatk-sv

gcsproxy

Reverse proxy for Google Cloud Storage

gnomad-browser

Explore gnomAD datasets on the web

gnomad_methods

Hail helper functions for the gnomAD project and Translational Genomics Group

hail

Scalable genomic data analysis.

hail-batch-test

hgdp

Scripts and analyses related to the Human Genome Diversity Project

images

Reusable single-software docker images

joint-calling

Sample and variant QC, based on https://github.com/broadinstitute/gnomad_qc

large-cohort-pipeline

Combine GVCFs and run QC