Homologous Recombination Deficiency
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DRAGEN Homologous Recombination Deficiency (HRD) Scoring takes in allele-specific copy number calls in either VCF format or directly streamed from somatic copy number callers. DRAGEN HRD then calculates scores for Loss of Heterozygosity (LOH), Telomeric Allelic Imbalance (TAI), and Large-Scale State Transition (LST). The three scores are output to the .hrdscore.csv file. This file is only created if HRD Scoring analysis was successful. In the event of insufficient CNV segmentation input to HRD, such as in cases of very low coverage or low confidence in tumor purity estimate, an error message will be logged and the output file for HRD is not created. DRAGEN HRD can be enabled whenever allele specific copy number (ASCN) events are available from DRAGEN CNV analysis. This is supported by DRAGEN CNV in WGS and WES workflows, both in tumor normal or tumor only mode.
For more information about enabling allele specific copy number analysis in somatic DRAGEN CNV workflows, please refer to the following user guide sections:
Use the following command-line options to run HRD scoring. You can run HRD scoring with somatic CNV calling or after using somatic CNV calling results.
To run HRD scoring together with somatic CNV calling, use the following options. For more CNV parameters, please refer to CNV calling.
--enable-hrd=true Set to true to enable HRD scoring to quantify genomic instability.
--enable-cnv=true Set to true to enable CNV calling to run together with HRD scoring.
To run HRD scoring after somatic CNV calling, use the following options:
--enable-hrd=true Set to true to enable HRD scoring to quantify genomic instability.
--hrd-input-ascn Specify the allele-specific copy number file (*cnv.vcf.gz). The CNV VCF file should include REF calls for proper HRD segmentation. See the option --cnv-enable-ref-calls in the CNV section.
--hrd-input-tn Specify the tumor normalized bin count file (*.tn.tsv.gz).
If reference is failed to AutoDetected, then centromere and blacklist files should be specified with following options:
--hrd-input-centromere Centromere locations per chromosome in tsv format
--hrd-input-blacklist Blacklist bed file
The following metrics are included in the .hrdscore.csv output file. The following is an example output file.
Sample
16
17
28
61
The following example command runs HRD end to end workflow with CNV. This is an example of Somatic WGS T/N. See the Somatic CNV section for other use cases. HRD is supported for any CNV workflows that support ASCN, and just needs to add --enable-hrd=true on top of the CNV command lines.
The following example command runs HRD standalone.
