DRAGEN Reference Support
DRAGEN supports the construction of a reference hash tables for both human and non-human reference genomes. The reference autodetect feature of DRAGEN is able to recognize the reference hash tables build on the four Human reference genomes: hg19 (hg19), GRCh37/hs37d5 (hs37d5), GRCh38/hs38d1(hg38), and T2T-CHM13v2.0 (chm13). Pre-built human reference hash tables are available for download at DRAGEN Software Support Site page.
DRAGEN also supports multigenome reference graphs hash tables which extend the reference genomes with alternative variant paths from a sample cohort used to construct the multigenome reference. A graph-based reference improves the mapping accuracy of Illumina reads in the “Difficult-to-Map Regions” of the genome and the downstream variant calling. Pre-built human multigenome reference graphs are available for download at DRAGEN Software Support Site page.
In the following tables we summarize the reference support for each DRAGEN component and the recommended reference type for each component.
Germline
| Component | Human hg19 | Human hs37d5 | Human hg38 | Human chm13 | Non-Human | Recommended Human Reference Type | Recommended Non-Human Reference Type |
|---|---|---|---|---|---|---|---|
SNV | Yes | Yes | Yes | Yes | Yes | Graph | Non-Graph |
CNV | Yes | Yes | Yes | Yes* | No | Graph | Non-Graph |
SV | Yes | Yes | Yes | Yes* | Yes | Graph | Non-Graph |
Expansion Hunter | Yes | Yes | Yes | No | No | Graph | Non-Graph |
Targeted Callers | Yes | Yes | Yes | No | No | Graph | Non-Graph |
RNA | Yes | Yes | Yes | Yes* | Yes | Non-Graph | Non-Graph |
De Novo | Yes | Yes | Yes | Yes* | Yes | Graph | Non-Graph |
Joint Genotyping | Yes | Yes | Yes | Yes* | Yes | Graph | Non-Graph |
Biomarkers (HLA) | Yes | Yes | Yes | Yes* | No | Graph | Non-Graph |
gVCF genotyper | Yes | Yes | Yes | Yes* | Yes | Graph | Non-Graph |
Somatic
| Component | Human hg19 | Human hs37d5 | Human hg38 | Human chm13 | Non-Human | Recommended Human Reference Type | Recommended Non-Human Reference Type |
|---|---|---|---|---|---|---|---|
SNV | Yes | Yes | Yes | Yes* | No | Non-Graph | Non-Graph |
UMI SNV | Yes | Yes | Yes | Yes* | No | Non-Graph | Non-Graph |
CNV | Yes | Yes | Yes | Yes* | No | Non-Graph | Non-Graph |
SV | Yes | Yes | Yes | Yes* | No | Non-Graph | Non-Graph |
Methylation
| Component | Human hg19 | Human hs37d5 | Human hg38 | Human chm13 | Non-Human | Recommended Human Reference Type | Recommended Non-Human Reference Type |
|---|---|---|---|---|---|---|---|
Methylation | Yes | Yes | Yes | No | No | Non-Graph | Non-Graph |
Annotation
| Component | Human hg19 | Human hs37d5 | Human hg38 | Human chm13 | Non-Human | Recommended Human Reference Type | Recommended Non-Human Reference Type |
|---|---|---|---|---|---|---|---|
Nirvana | Yes | Yes | Yes | No | Yes |
* DRAGEN supports the component execution, however the component's accuracy has not been established.
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