Structural Variant De Novo Quality Scoring

You can enable de novo structural variant quality scoring in DRAGEN.

To enable de novo scoring for structural variant joint diploid calling, set --sv-denovo-scoring to true. To adjust the threshold value for which variants are classified as de novo, use the --sv-denovo-threshold command line option. See DN Field for more information.

Inputs

De novo scoring requires the following two files:

• A pedigree file that specifies the relationship of all samples in the pedigree.
• The VCF output from germline structural variant calling analysis run jointly over all samples in the pedigree.

The pedigree file is required for de novo scoring. Use the same file format as required for joint small variant calling analysis and de novo scoring. For information on the file format, see Small Variant De Novo Calling. The file specifies which sample in the trio is the proband, mother, or father. If there are multiple trios specified in the pedigree file (eg, multigeneration pedigree or siblings), DRAGEN automatically detects the trios and provides the de novo scores on the proband sample of each detected trio.

DRAGEN applies de novo scoring to the VCF output from germline structural variant analysis for all samples specified in the pedigree file. You can supply the VCF file directly using the command line or produce the file as part of the DRAGEN run where de novo scoring is enabled.

Output

De novo scoring adds the de novo quality score (DQ) and de novo call (DN) fields for each sample in the output VCF file.

The DQ field is defined as follows.

##FORMAT=<ID=DQ,Number=1,Type=Float,Description="Denovo quality">

The DQ field represents the Phred-scaled posterior probability of the variant being de novo in the proband. For example, DQ scores of 13 and 20 correspond to a posterior probability of a de novo variant of 0.95 and 0.99. If DRAGEN can calculate the DQ score, the score is added to the proband samples. If the DQ score cannot be calculated, the field is set to ".".

The DN field is defined as follows.

##FORMAT=<ID=DN,Number=1,Type=String,Description="Possible values are 'DeNovo' or 'LowDQ'. Threshold for a passing de novo call is DQ >= 20">

DRAGEN compares valid (> 0) DQ scores against a threshold value. You can set the threshold value using the --sv-denovo-threshold command line option. For example, to set the threshold value to 10, add --sv-denovo-threshold 10 to the command line. The default threshold value is 20.

If a DQ score is greater than or equal to the threshold value, the DN field is set to DeNovo. If the DQ score is below the threshold value, the DN field is set to LowDQ. If the DQ is 0 or ". ", the DQ score is invalid and the DN field is set to ".".

De Novo Scoring Workflows

You can use de novo structural variant scoring in the following workflows.

• Perform de novo scoring in two DRAGEN runs. In the first, run germline structural variant analysis jointly over all samples in the pedigree file. In the second, apply de novo structural variant scoring to the joint germline VCF output. See Two-Run Workflow.
• Perform de novo scoring in one DRAGEN run. Run germline structural variant analysis jointly over all samples in the pedigree file, and then apply de novo scoring to the joint germline structural variant calls. See One-Run Workflow.

In the two-run workflow, first run a standard DRAGEN joint germline analysis over multiple samples as shown in the following example.

dragen -f \

--ref-dir <HASH_TABLE> \

--bam-input <BAM1> \

--bam-input <BAM2> \

--bam-input <BAM3> \

--enable-map align false \

--enable-sv true \

--output-directory <OUT_DIR1> \

--output-file-prefix <PREFIX1>

In the second run, use the VCF output (<OUT_DIR1>/<PREFIX1>.sv.vcf.gz) as input for de novo scoring. You can provide the VCF input using the --variant option. The following command line provides an example of the second run.

dragen -f \

--variant <MULTI_SAMPLE_VCF_FILE> \

--pedigree-file <PED_FILE> \

--enable-map-align false \

--sv-denovo-scoring true \

--output-directory <OUT_DIR2> \

--output-file-prefix <PREFIX2>

The resulting output VCF file (<OUT_DIR2>/<PREFIX2>.sv.vcf.gz) includes all de novo scoring annotations.

Run a standard DRAGEN joint germline analysis over multiple samples with all required de novo scoring options. The following example shows the one-run workflow.

dragen -f \

--ref-dir <HASH_TABLE> \

--bam-input <BAM1> \

--bam-input <BAM2> \

--bam-input <BAM3> \

--enable-map align=false \

--enable-sv=true \

--output-directory <OUT_DIR> \

--output-file-prefix <PREFIX> \

--sv-denovo-scoring true \

--pedigree-file <PED_FILE>

The resulting output VCF file (<OUT_DIR>/<PREFIX>.sv.vcf.gz) includes all de novo scoring annotations.