GATK Structural Variation (SV) Data

bioinformatics biology cromwell gatk-sv genetic genomic life sciences structural variation

Description

This dataset holds the data needed to run a structural variation discovery pipeline for Illumina short-read whole-genome sequencing (WGS) data in AWS.

Update Frequency

Every 3 months

License

https://github.com/LokaHQ/aws-open-data/blob/main/LICENSE

Documentation

https://github.com/LokaHQ/aws-open-data/blob/main/gatk-sv/documentation.md

Managed By

Loka Inc.

See all datasets managed by Loka Inc..

Contact

awsdata@loka.com

How to Cite

GATK Structural Variation (SV) Data was accessed on DATE from https://registry.opendata.aws/gatk-sv-data.

Usage Examples

Tutorials
Tools & Applications

Resources on AWS

  • Description
    This dataset contains, among others, the following data:
      • Illumina short-read whole-genome CRAMs or BAMs, aligned to hg38 with bwa-mem. BAMs must also be indexed.
      • Indexed GVCFs produced by GATK HaplotypeCaller, or a jointly genotyped VCF.
      • Family structure definitions file in PED format.
      • Reference files from the human reference genome Hg38.
    Resource type
    S3 Bucket
    Amazon Resource Name (ARN)
    arn:aws:s3:::gatk-sv-data-us-east-2
    AWS Region
    us-east-2
    AWS CLI Access (No AWS account required)
    aws s3 ls --no-sign-request s3://gatk-sv-data-us-east-2/
  • Description
    This dataset contains, among others, the following data:
      • Illumina short-read whole-genome CRAMs or BAMs, aligned to hg38 with bwa-mem. BAMs must also be indexed.
      • Indexed GVCFs produced by GATK HaplotypeCaller, or a jointly genotyped VCF.
      • Family structure definitions file in PED format.
      • Reference files from the human reference genome Hg38.
    Resource type
    S3 Bucket
    Amazon Resource Name (ARN)
    arn:aws:s3:::gatk-sv-data-us-east-1
    AWS Region
    us-east-1
    AWS CLI Access (No AWS account required)
    aws s3 ls --no-sign-request s3://gatk-sv-data-us-east-1/

Edit this dataset entry on GitHub

Tell us about your project

Home