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Genomics

Resources to better understand the genomic dataset and how to analyze it.

Working with Genomic Data

  • How the All of Us Genomic and mulit-omics data are organized
  • All of Us Pharmacogenomics (Star Allele) Calling
  • Smaller Callsets for Analyzing Short Read WGS SNP & Indel Data with Hail MT, VCF, and PLINK
  • Getting Started with Genomic Analyses on the Researcher Workbench
  • Variant Annotation Table
  • The new VariantDataset (VDS) format for All of Us short read WGS data

See all 8 articles

Information About Genomic Data Quality

  • All of Us Genomics & Multi-omics Quality Report
  • Benchmarking and quality analyses on the All of Us short-read structural variant catalog

Batch Processing and Workflows

  • How to use Anaconda in the Researcher Workbench
  • Using Docker Images on the Workbench
  • Overview of Batch Processing
  • How to use Cromwell in the All of Us Researcher Workbench
  • Workflows in the All of Us Researcher Workbench: Nextflow and Cromwell
  • Use dsub in the All of Us Researcher Workbench

Archived Genomic Articles

  • All of Us Genomic Quality Report (Archived C2024Q3R9 - v8)
  • Benchmarking and quality analyses on the All of Us Short-Read Structural Variant Catalog (v7)(ARCHIVED)
  • All of Us Genomic Quality Report (Archived C2022Q4R13 CDRv7)
  • How the All of Us Genomic data are organized (Archived CDRv8)
  • All of Us Genomic Quality Report (ARCHIVED C2022Q4R9 CDR v7)
  • Controlled CDR Directory (Archived CDRv8)

See all 16 articles

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