How to I prepare metrics files generated by DRAGEN to be used as input for Emedgene

When creating Emedgene cases that start from VCF, you can create a browsable DRAGEN report from the DRAGEN metrics files\

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

2. Define sample name as a variable

samplename="NA12878"

1. Combine the findand 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

{
    "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