DRAGEN Reference Support
DRAGEN supports the construction of 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
).
DRAGEN supports pangenome reference hash tables which extend the reference genomes with alternative variant paths from a sample cohort used to construct the pangenome reference. A pangenome-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 references are available for download at DRAGEN Software Support Site page.
The pangenome is the recommended for Germline human analyses. The accuracy achieved with pangenome references are highlighted in the plot below.

In the following tables we summarize the reference support for each DRAGEN component and the recommended reference type for each component.
Germline
Recommended reference type per component
SNV
Pangenome
Linear
CNV
Pangenome
Linear
SV
Pangenome
Linear
Expansion Hunter
Pangenome
Linear
Targeted Callers
Pangenome
Linear
RNA
Linear
Linear
De Novo
Pangenome
Linear
Joint Genotyping
Pangenome
Linear
Biomarkers (HLA)
Pangenome
Linear
gVCF genotyper
Pangenome
Linear
Component support
SNV
Yes
Yes
Yes
Yes
Yes
CNV
Yes
Yes
Yes
Yes*
Yes
SV
Yes
Yes
Yes
Yes*
Yes
Expansion Hunter
Yes
Yes
Yes
No
No
Targeted Callers
Yes
Yes
Yes
No
No
RNA
Yes
Yes
Yes
Yes*
Yes
De Novo
Yes
Yes
Yes
Yes*
Yes
Joint Genotyping
Yes
Yes
Yes
Yes*
Yes
Biomarkers (HLA)
Yes
Yes
Yes
Yes*
No
gVCF genotyper
Yes
Yes
Yes
Yes*
Yes
Somatic
Recommended reference type per component
SNV
Linear
Linear
UMI SNV
Linear
Linear
CNV
Linear
Linear
SV
Linear
Linear
Component support
SNV
Yes
Yes
Yes
Yes*
No
UMI SNV
Yes
Yes
Yes
Yes*
No
CNV
Yes
Yes
Yes
Yes*
No
SV
Yes
Yes
Yes
Yes*
No
Methylation
Recommended reference type per component
Methylation
Linear
Linear
Component support
Methylation
Yes
Yes
Yes
No
No
Annotation
Recommended reference type per component
Nirvana
Pangenome
Linear
Component support
Nirvana
Yes
Yes
Yes
No
Yes
* DRAGEN supports the component execution, however the component's accuracy has not been established.
By default, DRAGEN will error out if a linear reference is provided when running a component for which a pangemome reference is recommended as listed in the above table. If the user is sure that a linear reference is reference is desired, the error can be suppressed by setting --validate-pangenome-reference=false
.
See Prepare a Reference Genome for how to build a custom reference genome.
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