Pinned Repositories
analysis-runner
automated-interpretation-pipeline
Rare Disease variant prioritisation MVP
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-cost-control
A Cloud Function to handle GCP billing budget notifications.
cpg-infrastructure
This repository is used to manage the infrastructure at the CPG
cuKING
CUDA-based KING relatedness estimation
metamist
Sample level metadata system
production-pipelines
Genomics workflows for CPG using Hail Batch
rare-disease
A collection of scripts relating to rare-disease specific projects
seqr
web-based analysis tool for rare disease genomics
Centre for Population Genomics's Repositories
populationgenomics/automated-interpretation-pipeline
Rare Disease variant prioritisation MVP
populationgenomics/production-pipelines
Genomics workflows for CPG using Hail Batch
populationgenomics/cpg-infrastructure
This repository is used to manage the infrastructure at the CPG
populationgenomics/seqr
web-based analysis tool for rare disease genomics
populationgenomics/analysis-runner
populationgenomics/rare-disease
A collection of scripts relating to rare-disease specific projects
populationgenomics/ClinvArbitration
A side-project from the AIP, containing the code, logic, and documentation for the ClinVar consequence reassessment process in use at the CPG
populationgenomics/hail
Scalable genomic data analysis.
populationgenomics/images
Reusable single-software docker images
populationgenomics/metamist
Sample level metadata system
populationgenomics/references
Reference data for bioinformatics workflows
populationgenomics/sv-workflows
Structural Variation Workflows
populationgenomics/team-docs
Documentation, guides, tips and tricks when working at the CPG
populationgenomics/variant-curation-portal
Web application for curating loss of function variants
populationgenomics/saige-tenk10k
Hail batch pipeline to run SAIGE on CPG's GCP
populationgenomics/tob-wgs
Tasmanian Ophthalmic Biobank Whole Genome Sequencing Project
populationgenomics/cpg-methods
Methods developed by the Centre for Population Genomics
populationgenomics/cpg-python-template-repo
A template repository for python code, implementing the CPG setup guidelines
populationgenomics/cpg-utils
Library of convenience functions specific to the CPG
populationgenomics/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.
populationgenomics/exome-results-browsers
Results browsers for case-control studies of psychiatric diseases done at the Broad Institute
populationgenomics/gnomad-browser
Explore gnomAD datasets on the web
populationgenomics/gnomad_methods
Hail helper functions for the gnomAD project and Translational Genomics Group
populationgenomics/mocha-wgs
A WDL workflow for running MoChA on WGS data
populationgenomics/mrff-cnv-reanalysis
populationgenomics/ourdna
populationgenomics/pre-commits
Repository of common pre-commit hooks
populationgenomics/renovate-test
populationgenomics/sgs-somatic-mutation
Genomic Medicine Lab repository for somatic variant analysis
populationgenomics/TRTools
Toolkit for genome-wide analysis of tandem repeats