1000 Genomes Phase 3 Reanalysis with DRAGEN 3.5 and 3.7

Description

This dataset contains alignment files and short nucleotide, copy number, repeat expansion (STR) and structural variant call files from the 1000 Genomes Project Phase 3 dataset (n=3202) using Illumina DRAGEN v3.5.7b and v3.7.6 software. The v3.7.6 dataset also includes results from joint small variant, de novo structural variant, de novo copy number variant and repeat expansion calls on 602 trio families comprised of members from the 1000 Genomes Project Phase 3 dataset, as well as DRAGEN gVCF Genotyper (v3.8.3) analysis on the entire dataset (n=3202). Improvements and new features in the v3.7.6 individual samples analyses include CYP2D6 variant calling and joint detection (see ‘DRAGEN 3.7 User Guide’ for details on these features) and use of graph-based hg19 and hg38 reference hash tables (see ‘DRAGEN Wins at PrecisionFDA Truth Challenge V2 Showcase Accuracy Gains from Alt-aware Mapping and Graph Reference Genomes’ for details).

Update Frequency

Files may be updated subsequent to changes to the 1000 Genomes Project data set or select new DRAGEN features or offerings.

License

TBD

Documentation

DRAGEN Support Resources

Managed By

Illumina, Inc.

See all datasets managed by Illumina, Inc..

Contact

Illumina, Inc.

How to Cite

1000 Genomes Phase 3 Reanalysis with DRAGEN 3.5 and 3.7 was accessed on DATE from https://registry.opendata.aws/ilmn-dragen-1kgp.

Usage Examples

Tutorials

• DRAGEN Quick Start on AWS by AWS Quick Start Team
  

Tools & Applications

• DRAGEN 3.7 User Guide by Illumina Inc.
  
• DRAGEN 3.7.5b Release by Illumina Inc.
  
• DRAGEN on BaseSpace Sequence Hub by Illumina Inc.
  

Publications

• DRAGEN Wins at PrecisionFDA Truth Challenge V2 Showcase Accuracy Gains from Alt-aware Mapping and Graph Reference Genomes by Illumina Inc. (2021)
  
• precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions (Preprint) by Olson et al (2020)