DRAGEN Reference Support
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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 .
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.
SNV
Pangenome
Linear
Yes
Yes
Yes
Yes
Yes
CNV
Pangenome
Linear
Yes
Yes
Yes
Yes*
No
SV
Pangenome
Linear
Yes
Yes
Yes
Yes*
Yes
Expansion Hunter
Pangenome
Linear
Yes
Yes
Yes
No
No
Targeted Callers
Pangenome
Linear
Yes
Yes
Yes
No
No
RNA
Linear
Linear
Yes
Yes
Yes
Yes*
Yes
De Novo
Pangenome
Linear
Yes
Yes
Yes
Yes*
Yes
Joint Genotyping
Pangenome
Linear
Yes
Yes
Yes
Yes*
Yes
Biomarkers (HLA)
Pangenome
Linear
Yes
Yes
Yes
Yes*
No
gVCF genotyper
Pangenome
Linear
Yes
Yes
Yes
Yes*
Yes
SNV
Linear
Linear
Yes
Yes
Yes
Yes*
No
UMI SNV
Linear
Linear
Yes
Yes
Yes
Yes*
No
CNV
Linear
Linear
Yes
Yes
Yes
Yes*
No
SV
Linear
Linear
Yes
Yes
Yes
Yes*
No
Methylation
Linear
Linear
Yes
Yes
Yes
No
No
Nirvana
Pangenome
Linear
Yes
Yes
Yes
No
Yes
* DRAGEN supports the component execution, however the component's accuracy has not been established.
See for how to build a custom reference genome.
