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8000+ New WGS Variant Calls Now Available in the GDC!

The GDC is excited to announce the release of 8000+ new whole genome sequencing (WGS) variant calls as part of Data Release 42. Highlights of this release include:

  • New WGS Variants: New WGS variant calls for The Cancer Genome Atlas (TCGA) and other programs, featuring:
    • GATK4 MuTect2 and SvABA simple and annotated somatic mutations 
    • GATK4 copy number segments 
    • SvABA and Manta structural variants
  • Comprehensive Update to TCGA Clinical Data - TCGA clinical data previously available only in supplemental files is now accessible for download and querying through the GDC Data Portal and API
  • Higher Coverage WGS Alignments: Over 1,500 new higher-coverage TCGA WGS alignments across multiple TCGA projects
  • Expanded RNA-Seq and miRNA-Seq Data:
    • RNA-Seq data for TCGA Lung Squamous Cell Carcinoma (LUSC) and Glioblastoma Multiforme (GBM) projects 
    • miRNA-Seq data for TCGA LUSC, GBM, and Ovarian Carcinoma (OV) projects
  • TARGET Program Updates: Updated RNA-Seq data for Acute Myeloid Leukemia (AML) and WGS data for Neuroblastoma (NBL)
  • Tumor Purity and Ploidy Migration: Tumor purity and ploidy have been migrated from aligned reads to copy number segments

For detailed information on GDC WGS data harmonization workflows, visit the GDC Documentation Site. A full list of updates can be found in the Data Release 42.0 Notes.