GATK Structural Variation (SV) Data

Stream data with DDA:

from dagshub.streaming import DagsHubFilesystem

fs = DagsHubFilesystem(".", repo_url="https://dagshub.com/DagsHub-Datasets/gatk-sv-data-dataset")

fs.listdir("s3://gatk-sv-data-us-east-2")

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.

Contact:

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

Managed By:

https://loka.com/

Resources:

1. resource:
   • 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.

- ARN: arn:aws:s3:::gatk-sv-data-us-east-2
- Region: us-east-2
- Type: S3 Bucket

2. resource:
   • 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.

- ARN: arn:aws:s3:::gatk-sv-data-us-east-1
- Region: us-east-1
- Type: S3 Bucket

Tags:

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

Tutorials:

1. tutorial:
   • Title: AWS Setup & Execution
   • URL: https://github.com/goldfinchbio/aws-gatk-sv
   • AuthorName: Goldfinch Bio and Loka Inc.

Tools & Applications:

1. tools & applications:
   • Title: Structural Variant Analysis on AWS with Amazon FSx for Lustre
   • URL: https://aws.amazon.com/blogs/industries/using-structural-variant-analysis-on-aws-with-amazon-fsx-for-lustre-in-novel-therapeutic-discovery/
   • AuthorName: Goldfinch Bio and Loka Inc.