Prepare QC files for a NGS VCF case

When creating NGS 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 the local directory that contains the metrics files for a specific sample.

2

Define the sample name as a variable:

samplename="NA12878"

3

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:

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"

4

Upload the metrics.tar.gz file to the storage location used for case creation.

5

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

{
    "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
}