1000 Genomes Phase 3 Reanalysis with DRAGEN 3.5 – Data Lakehouse Ready Dataset for Machine Learning
Install DagsHub:
pip install dagshubTo stream this data directly on DagsHub
from dagshub.streaming import DagsHubFilesystem
fs = DagsHubFilesystem(".", repo_url="https://dagshub.com/DagsHub-Datasets/1000-genomes-data-lakehouse-ready-dataset")
fs.listdir("s3://aws-roda-hcls-datalake/thousandgenomes_dragen")Description
The 1000 Genomes Project is an international collaboration which has established the most detailed catalogue of human genetic variation, including SNPs, structural variants, and their haplotype context. There were a total of 3202 individuals sequenced as part of Phase 3 of this project. The high coverage samples were processed using the Illumina DRAGEN v3.5.7b pipeline and are available at s3://1000genomes-dragen/. This dataset contains the VCFs transformed to Parquet/ORC in 3 different schemas – partitioned by samples, partitioned by chromosome and a nested data format. These representations of the 1000 Genomes DRAGEN data are stored in Parquet/ORC format and can be queried through Amazon Athena. To add these tables to your Glue Data Catalog and for sample queries on this dataset, please refer to the link in our Documentation.
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License
Data from the 1000 Genomes Project is now available without embargo, following the final publication from the project. Use of the data should be cited in the usual way, with current details available at http://www.internationalgenome.org/faq/how-do-i-cite-1000-genomes-project.