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 – 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 6 target PGx genes across 9 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	Global Diversity Array with Enhanced PGx (Product Files) See Pharmacogenomic Analysis for semi-custom arrays for further detail.
Related Local Commands	Genotype Call Genotype GTC-to-VCF [optional] 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] • 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] • CNV VCF File • BedGraph File [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	Global Diversity Array with Enhanced PGx (Product Files) See Pharmacogenomic Analysis for semi-custom arrays for further detail.
Related Local Commands	Genotype call Genotype GTC-to-VCF [optional] Copy-number call Star-allele call 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] • 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] • CNV VCF File • BedGraph File [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, with known limitations when sample sheet is used.
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.