DRAGEN Array Applications

The following Types of Analysis are currently supported by DRAGEN Array:

• DRAGEN Array – Genotyping

• DRAGEN Array – PGx – CNV calling

• DRAGEN Array – PGx – Star allele annotation

• DRAGEN Array – Methylation QC

• DRAGEN Array – CNV and LOH Calling

Product & Analysis Compatibility

These products/beadchips have been verified to be compatible with the following analyses and versions of DRAGEN Array:

Manifest Name	DRAGEN Array Cloud Version(s)	DRAGEN Array Local Version(s)	Analysis	Genome(s)
BovineSNP50_v3_A	v1.0, v1.1	v1.0+	DRAGEN Array – Genotyping	UMD3
GDA-8v1-0_D	v1.0, v1.1	v1.0+	DRAGEN Array – Genotyping	GRCh37, GRCh38
GDA_PGx-8v1-0_20042614_E	v1.0, v1.1	v1.0+	DRAGEN Array – Genotyping	GRCh37, GRCh38
GDA_PGx-8v1-0_20042614_E	v1.0, v1.1	v1.0+	DRAGEN Array – PGx – CNV calling	GRCh37, GRCh38
GDA_PGx-8v1-0_20042614_E	v1.0	v1.0	DRAGEN Array – PGx – Star allele annotate	GRCh38
GDA_PGx-8v1-0_20042614_G	v1.0, v1.1	v1.0+	DRAGEN Array – Genotyping	GRCh38
GDA_PGx-8v1-0_20042614_G	v1.0, v1.1	v1.0+	DRAGEN Array – PGx – CNV Calling	GRCh38
GDA_PGx-8v1-0_20042614_G	v1.1+	v1.1+	DRAGEN Array – PGx – Star allele annotate	GRCh38
GSA-24v3-0_A	v1.0, v1.1	v1.0+	DRAGEN Array – Genotyping	GRCh37, GRCh38
GSA-PGx-48v4-0_20079540_E	v1.0, v1.1	v1.0+	DRAGEN Array – Genotyping	GRCh38
GSA-PGx-48v4-0_20079540_E	v1.0, v1.1	v1.0+	DRAGEN Array – PGx – CNV Calling	GRCh38
GSA-PGx-48v4-0_20079540_E	v1.1+	v1.1+	DRAGEN Array – PGx – Star allele annotate	GRCh38
GCRA-PGx-24v1-0_20084467_C	v1.0, v1.1	v1.0+	DRAGEN Array – Genotyping	GRCh38
GCRA-PGx-24v1-0_20084467_C	v1.0, v1.1	v1.0+	DRAGEN Array – PGx – CNV Calling	GRCh38
GCRA-PGx-24v1-0_20084467_C	v1.1+	v1.1+	DRAGEN Array – PGx – Star allele annotate	GRCh38
PRSbooster_20083382_A	v1.1+	v1.0+	DRAGEN Array – Genotyping	GRCh37
EPIC-8v1-0_B5	v1.0	N/A	DRAGEN Array – Methylation – QC	GRCh38
EPIC-8v2-0_A2	v1.0	N/A	DRAGEN Array – Methylation – QC	GRCh38
MSA-48v1-0_20102838_A1	v1.0	N/A	DRAGEN Array – Methylation – QC	GRCh38
CytoSNP-850Kv1-4_iScan_B	v1.2	v1.2	DRAGEN Array – CNV and LOH Calling – 1.2.0	GRCh37, GRCh38
GSACyto-24v1_20044998_C	v1.2	v1.2	DRAGEN Array – CNV and LOH Calling – 1.2.0	GRCh37, GRCh38
GDACyto-8v1-0_20047166_E	v1.2	v1.2	DRAGEN Array – CNV and LOH Calling – 1.2.0	GRCh37, GRCh38

DRAGEN Array – Genotyping

Item	Description
Summary	Provides genotyping results for any human Infinium genotyping array.
Variant types detected	SNV Indel
Sample minimum	1 sample
Arrays supported	Any human Infinium genotyping array including custom and semi-custom to create a SNV VCF output. Illumina provides Genome FASTA Files required to map to the reference genome for human, genome build 37 and 38. DRAGEN Array Cloud offers additional output formats including Locus Summary and Final Report which are applicable for Infinium arrays for human and non-human species.
Related Local Commands	genotype call genotype gtc-to-vcf
Related Cloud Specifics	Select Type of Analysis DRAGEN Array – Genotyping from the dropdown. Max 1152 samples are supported.
Inputs	• IDAT(s) • Manifest Files [may be pre-setup on cloud] • Cluster File [may be pre-setup on cloud] • Genome FASTA Files [pre-setup on cloud] • Sample Sheet [optional on cloud and local]
Outputs	Per sample: • Genotype Call (GTC) File • SNV VCF File [optional on cloud and local] • TBI Index File [optional on cloud and local] Per analysis batch: • Genotype Summary Files • Final Report [cloud only] • Locus Summary [cloud only] • Warning/Error Messages
Cost	Local: No cost download from Illumina Support Site. Cloud: iCredits to analyze and store data as needed.

DRAGEN Array – PGx – CNV calling

Item	Description
Summary	Provides CNV calling on 7 target PGx genes across 10 target regions, plus genotyping outputs.
Variant types detected	SNV Indel CNV
Sample minimum	Minimum of 24 samples with 22 passing QC defined as Log R Dev < 0.2. 96 samples are recommended for best results.
Arrays supported	Check Product & Analysis Compatibility here Product & Analysis Compatibility See Pharmacogenomic Analysis for semi-custom arrays for further detail.
Related Local Commands	genotype call genotype gtc-to-vcf [optional] pgx copy-number call
Related Cloud Specifics	Select Type of Analysis DRAGEN Array – PGx – CNV calling from the dropdown. Max 384 samples are supported.
Inputs	• IDAT(s) • Manifest Files [may be pre-setup on cloud] • Cluster File [may be pre-setup on cloud] • Genome FASTA Files [pre-setup on cloud] • PGx CN Model File [pre-setup on cloud] • Sample Sheet [optional on cloud and local]
Outputs	Per sample: • Genotype Call (GTC) File • SNV VCF File [optional on local] • TBI Index File [optional on local] • PGx CNV VCF File • BedGraph Files [optional on local] Per analysis batch: • Genotype Summary Files • CN Summary File • Copy Number Batch File • Warning/Error Messages
Cost	Local: No cost download from Illumina Support Site. Cloud: iCredits to analyze and store data as needed.

DRAGEN Array – PGx – Star Allele Annotation

Item	Description
Summary	Provides PGx annotation on over 50 genes, plus PGx CNV and genotyping outputs
Variant types detected	SNV Indel CNV Star allele diplotype
Sample minimum	Minimum of 24 samples with 22 passing QC defined as Log R Dev < 0.2. 96 samples are recommended for best results.
Arrays supported	Check Product & Analysis Compatibility here Product & Analysis Compatibility See Pharmacogenomic Analysis for semi-custom arrays for further detail.
Related Local Commands	genotype call genotype gtc-to-vcf pgx copy-number call pgx star-allele call pgx star-allele annotate
Related Cloud Specifics	Select Type of Analysis DRAGEN Array – PGx – Star Allele Annotation from the dropdown. Max 384 samples are supported.
Inputs	• IDAT(s) • Manifest Files [may be pre-setup on cloud] • Cluster File [may be pre-setup on cloud] • Genome FASTA Files [pre-setup on cloud] • PGx CN Model File [pre-setup on cloud] • PGx Database File [pre-setup on cloud] • Sample Sheet [optional on cloud and local]
Outputs	Per sample: • Genotype Call (GTC) File • SNV VCF File [optional on local] • TBI Index File [optional on local] • PGx CNV VCF File • BedGraph Files [optional on local] • Star Allele JSON File Per analysis batch: • Star Allele CSV File • Genotype Summary Files • CN Summary File • Copy Number Batch File • Warning/Error Messages
Cost	Local: Per sample analysis. Cloud: Per sample analysis. iCredits to store data as needed. Visit the Illumina Product Page to learn more.

DRAGEN Array – Methylation QC

Item	Description
Summary	Provides methylation QC for Infinium methylation arrays.
Variant types detected	N/A
Sample minimum	1 sample
Arrays supported	Recommended thresholds and all built-in control probes are available for Methylation Screening Array (MSA) and MethylationEPIC (v1 & v2) originating from iScan. In non-human and custom arrays, availability of built-in QC probes may vary, and failure thresholds must be defined by the user.
Related Local Commands	Not available on DRAGEN Array Local.
Related Cloud Specifics	Select Type of Analysis DRAGEN Array – Methylation – QC from the dropdown. Adjust customizable thresholds as desired. Further detail can be found in Additional information for DRAGEN Array Methylation QC. A maximum of 1152 samples are supported.
Inputs	• IDAT(s) [from iScan instrument] • Manifest Files [may be pre-setup on cloud] • IDAT Sample Sheet [optional on cloud]
Outputs	Per sample: • Methylation Control Probe Output File • Methylation CG Output File Per analysis batch: • Methylation Sample QC Summary Files • Methylation Sample QC Summary Plots • Methylation Principal Component Summary • Methylation Manifest Files • Methylation Logs and Error Files
Cost	Cloud: iCredits to analyze and store data as needed.

DRAGEN Array – CNV and LOH Calling

Item	Description
Summary	Provides cytogenetic genome-wide copy number and loss of heterozygosity calling
Variant types detected	CNV LOH
Sample minimum	Minimum of 1 sample.
Arrays supported	Check Product & Analysis Compatibility here Product & Analysis Compatibility
Related Local Commands	genotype call genotype gtc-to-vcf [optional] genotype gtc-to-bedgraph cyto call cyto annotate
Related Cloud Specifics	Select Type of Analysis DRAGEN Array – CNV and LOH Calling from the dropdown. Max 1152 samples are supported.
Inputs	• IDAT(s) • Manifest Files [may be pre-setup on cloud] • Cluster File [may be pre-setup on cloud] • Cytogenetics Model File [pre-setup on cloud] • Cytogenetics Database File [only necessary for local] • IDAT Sample Sheet [optional]
Outputs	Per sample: • Genotype Call (GTC) File [optional on cloud] • SNV VCF File [optional on local and cloud] • TBI Index File [optional on local and cloud for snv vcf] • Cytogenetics CNV VCF File • Cytogenetics Annotation JSON File • BedGraph Files [optional on local] Per analysis batch: • Genotype Summary Files • Warning/Error Messages
Cost	Local: No cost download from Illumina Support Site. Cloud: iCredits to analyze and store data as needed. As well as additional sample-based costs if uploaded into the Emedgene interface.