> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/dragen-qc-report/prerequisites-for-accessing-the-dragen-qc-report/how-to-i-prepare-metrics-files-generated-by-dragen-to-be-used-as-input-for-emedgene.md).
# Prepare QC files for a NGS VCF case
When creating NGS cases that start from VCF, you can create a browsable [DRAGEN QC report](/emedgene/emedgene-analyze-manual/reviewing_a_case/lab_tab/sample-quality-section/dragen-qc-report.md) from the DRAGEN metrics files. Due to security restrictions, CSV files are not directly ingested, but they can be included when packaged in a TAR file.
{% stepper %}
{% step %}
Navigate to the local directory that contains the metrics files for a specific sample.
{% endstep %}
{% step %}
Define the sample name as a variable:
`samplename="NA12878"`
{% endstep %}
{% step %}
Combine the `find` and `tar` commands to package the files into a `*.metrics.tar.gz` file.
Use this command to find files matching the required patterns:
{% code overflow="wrap" %}
```bash
find . \( -name "*.csv" -o -name "*.tsv" -o -name "*.counts" -o -name "*.counts.gz" -o -name "*.counts.gc-corrected" -o -name "*.counts.gc-corrected.gz" -o -name "*.ploidy.vcf" -o -name "*.correlation.txt.gz" -o -name "*.correlation.txt" -o -name "*.repeats.vcf" -o -name "*.ploidy.vcf.gz" -o -name "*.repeats.vcf.gz" -o -name "*.annotated_cyto.json" \) | xargs tar -czf "${samplename}.metrics.tar.gz"
```
{% endcode %}
{% endstep %}
{% step %}
Upload the `metrics.tar.gz` file to the storage location used for case creation.
{% endstep %}
{% step %}
Add `metrics.tar.gz` to the case creation API JSON payload using the corresponding storage ID.
If the extension is not included in the filename, such as for files from BaseSpace, set `"sample_type": "dragen-metrics"` in the JSON payload.
Case creation API JSON
```json
{
"test_data":
{
"consanguinity": false,
"inheritance_modes":
[],
"sequence_info":
{},
"type": "Whole Genome",
"notes": "",
"samples":
[
{
"bam_location": "",
"fastq": "NA12878-PCRF450-1",
"status": "uploaded",
"directoryPath": "",
"sampleFiles":
[
{
"filename": "NA12878-PCRF450-1.metrics.tar.gz",
"sample_type": "dragen-metrics",
"path": "/analysis_output/demo_data_germline_v4_3_6_v2-DRAGEN_Germline_Whole_Genome_4-3-6-v2-75b081e8-a8aa-433e-862b-a20d2d65e492/NA12878-PCRF450-1/NA12878-PCRF450-1.metrics.tar.gz",
"size": 0,
"storage_id": 420,
"status": "uploaded",
"vcf_column_name": "NA12878-PCRF450-1",
"vcf_column_names":
[
"NA12878-PCRF450-1"
],
"loadingSample": false
},
{
"filename": "NA12878-PCRF450-1.hard-filtered.vcf.gz",
"sample_type": "vcf",
"path": "/analysis_output/demo_data_germline_v4_3_6_v2-DRAGEN_Germline_Whole_Genome_4-3-6-v2-75b081e8-a8aa-433e-862b-a20d2d65e492/NA12878-PCRF450-1/NA12878-PCRF450-1.hard-filtered.vcf.gz",
"size": 0,
"storage_id": 420,
"status": "uploaded",
"vcf_column_name": "NA12878-PCRF450-1",
"vcf_column_names":
[
"NA12878-PCRF450-1"
],
"loadingSample": false
}
],
"storage_id": 420,
"sampleType": "vcf"
}
],
"sample_type": "vcf",
"patients":
{
"proband":
{
"fastq_sample": "NA12878-PCRF450-1",
"gender": "Male",
"healthy": false,
"relationship": "Test Subject",
"notes": "",
"phenotypes":
[
{
"id": "phenotypes/EMG_PHENOTYPE_0001324",
"name": "Muscle weakness"
}
],
"detailed_ethnicity":
{
"maternal":
[],
"paternal":
[]
},
"zygosity": "",
"quality": "",
"dead": false,
"ignore": false,
"id": "proband"
},
"other":
[]
},
"diseases":
[],
"disease_penetrance": 100,
"disease_severity": "",
"boostGenes": false,
"selected_preset_set": "",
"incidental_findings": null,
"labels":
[],
"gene_list":
{
"type": "all",
"id": 1,
"visible": false
}
},
"should_upload": false,
"sharing_level": 0
}
```
{% endstep %}
{% endstepper %}
---
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