Requirements by case type

This page explains the requirements for viewing the DRAGEN QC report for each case type.

NGS FASTQ cases

Run a FASTQ case in Emedgene.

Result: Because DRAGEN analysis is integrated into Emedgene secondary analysis pipeline, QC reports are automatically generated in the system.

NGS VCF cases

Prerequisite: Batch case upload via UI or CLI or API-based case creation

1

Run DRAGEN analysis externally. This approach is referred to as "Bring your own DRAGEN (BYOD)".

2

Prepare the DRAGEN QC data. Use one of these options:

DRAGEN report HTML file (v100.40.0+): Download the DRAGEN report as a .report.html file per sample.

or

DRAGEN metrics TAR file: Download DRAGEN QC metrics files and prepare a TAR archive as described here.

3

Upload the HTML file or TAR archive together with the sample VCF file.

4

Run the case.

Result:

• If you uploaded an HTML file: The system directly visualizes the uploaded HTML file instead of generating the report from metrics files.

• If you uploaded a TAR file: The system generates an interactive HTML report from metrics files.

Array VCF cases

Array cases start from VCF input files.

Prerequisites:

• DRAGEN Array v1.3.0 and later

• Emedgene v100.39.0 and later

• Batch case upload via UI or CLI or API-based case creation

1

Run DRAGEN analysis externally. This approach is referred to as "Bring your own DRAGEN (BYOD)".

2

Prepare the DRAGEN QC data. Use one of these options:

DRAGEN report HTML file (v100.40.0+): Download DRAGEN report as a .report.html file per sample.

or

DRAGEN metrics files: Download the .annotated_cyto.json DRAGEN QC metrics file, the sample VCF file, and the .gt_sample_summary.json file.

3

Upload the HTML file or metrics files together with the sample VCF file.

4

Run the case.

Result:

• If you uploaded an HTML file: The system directly visualizes the uploaded HTML file instead of generating the report from metrics files.

• If you uploaded metrics files: The system generates an interactive HTML report from metrics files.