Which reference genomes can I use?

Both GRCh37/hg19 and GRCh38/hg38 are supported. To run cases using the GRCh38/hg38 reference genome, your pipeline version should be 5.24 or newer.

For Dragen version < 4.0, we are using the following files:

• hs37d5.fa.gz for GRCh37/hg19.

  Includes data from GRCh37, the rCRS mitochondrial sequence, Human herpesvirus 4 type 1 and the concatenated decoy sequences. Downloadable here.

• GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz for GRCh38/hg38.

  Contains the sequences of the chromosomes, the rCRS mitochondrial sequence, unlocalized scaffolds, and unplaced scaffolds. Downloadable here.

For Dragen version 4.0, we are using the following files:

• Multigenome Graph hg38+alt_masked+cnv+graph+hla+rna-8-r2.0 for GRCh38/hg38.

  Pre-built multigenome hash tables for hg38. The hash table builds include DNA, RNA, CNV, and HLA tables. Downloadable here. ​

• Multigenome Graph hs37d5-cnv.graph.hla.rna for GRCh37d5.

  Pre-built multigenome hash tables for GRCh37d5. The hash table builds include DNA, RNA, CNV, and HLA tables. Available on demand.

For Dragen version 4.2, we are using the following files:

• Multigenome Graph hg38-alt_masked.cnv.graph.hla.rna-9-r3.0 for GRCh38/hg38.

  Pre-built multigenome hash tables for hg38. The hash table builds include DNA, RNA, CNV, and HLA tables. Downloadable here. ​

• Multigenome Graph hs37d5-cnv.graph.hla.rna-9-r3.0 for GRCh37d5.

  Pre-built multigenome hash tables for GRCh37d5. The hash table builds include DNA, RNA, CNV, and HLA tables. Downloadable here.

Note: you can run cases with both reference genomes in the same organization.

Note: curated and historical data are automatically lifted over on the fly.

Don't miss our article on the matter!

Demystifying the Versions of GRCh38/hg38 Reference Genomes, How They are Used in DRAGEN and Their Impact on Accuracy