Prepare DRAGEN QC metrics files to be included in a VCF case

When creating Emedgene cases that start from VCF, you can create a browsable DRAGEN QC report 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.

1. Navigate to local directory containing metrics files for a specific sample.

2. Define sample name as a variable samplename="NA12878".

3. Combine the find and tar commands to package the files into a tar.gz file with the following extension *.metrics.tar.gz. Command to find files matching the required patterns:

find . \( -name "*.csv" -o -name "*.tsv" -o -name "*.counts" -o -name "*.counts.gz" -o -name "*.counts.gc-corrected" -o -name "*.counts.gc-corrected.gz" -o -name "*.ploidy.vcf" -o -name "*.repeats.vcf" -o -name "*.ploidy.vcf.gz" -o -name "*.repeats.vcf.gz" \) | xargs tar -czf "${samplename}.metrics.tar.gz"

1. Upload the metrics.tar.gz file to the storage location used for creating cases.

2. Add metrics.tar.gz to case creation API JSON payload using the corresponding storage ID. Ensure that if the extension is not contained in the filename (e.g. files from BaseSpace) that "sample_type": "dragen-metrics" is set within the JSON payload.

Case creation API 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
}

1. DRAGEN report link is then available once your case has been delivered.