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DRAGEN Array v1.1
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DRAGEN Array v1.1
  • Overview
    • Welcome to DRAGEN Array
    • DRAGEN Array Applications
  • Product Guides
    • DRAGEN Array Cloud Analysis
    • DRAGEN Array Local Analysis
    • Input Files
    • Output Files
  • Reference
    • Support and Additional Resources
    • Frequently Asked Questions
    • Release Notes
      • DRAGEN Array v1.1.0 Release Notes
      • DRAGEN Array v1.0.0 Release Notes
        • DRAGEN Array Genotyping Cloud v1.0.0 Release Notes
        • DRAGEN Array Methylation QC Cloud v1.0.0 Release Notes
    • PGx CNV Coverage
    • PGx Allele Definitions and PGx Guidelines
    • PGx Star Allele Coverage
    • Document Revision History
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  • Product & Analysis Compatibility
  • DRAGEN Array – Genotyping
  • DRAGEN Array - PGx – CNV calling
  • DRAGEN Array – PGx – Star Allele Annotation
  • DRAGEN Array – Methylation QC

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  1. Overview

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

Product & Analysis Compatibility

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

Product
DRAGEN Array Version(s)
Analysis
Genome(s)

BovineSNP50_v3_A

v1.0, v1.1

DRAGEN Array – Genotyping

UMD3

GDA-8v1-0_D

v1.0, v1.1

DRAGEN Array – Genotyping

GRCh37, GRCh38

GDA_PGx-8v1-0_20042614_E

v1.0, v1.1

DRAGEN Array – Genotyping

GRCh37, GRCh38

GDA_PGx-8v1-0_20042614_E

v1.0, v1.1

DRAGEN Array – PGx - CNV calling

GRCh37, GRCh38

GDA_PGx-8v1-0_20042614_E

v1.0

DRAGEN Array – PGx - Star allele annotate

GRCh38

GDA_PGx-8v1-0_20042614_G

v1.1

DRAGEN Array – Genotyping

GRCh38

GDA_PGx-8v1-0_20042614_G

v1.1

DRAGEN Array – PGx - CNV Calling

GRCh38

GDA_PGx-8v1-0_20042614_G

v1.1

DRAGEN Array – PGx - Star allele annotate

GRCh38

GSA-24v3-0_A

v1.0, v1.1

DRAGEN Array – Genotyping

GRCh37, GRCh38

GSA-PGx-48v4-0_20079540_E

v1.1

DRAGEN Array – Genotyping

GRCh38

GSA-PGx-48v4-0_20079540_E

v1.1

DRAGEN Array – PGx - CNV Calling

GRCh38

GSA-PGx-48v4-0_20079540_E

v1.1

DRAGEN Array – PGx - Star allele annotate

GRCh38

GCRA-PGx-24v1-0_20084467_C

v1.1

DRAGEN Array – Genotyping

GRCh38

GCRA-PGx-24v1-0_20084467_C

v1.1

DRAGEN Array – PGx - CNV Calling

GRCh38

GCRA-PGx-24v1-0_20084467_C

v1.1

DRAGEN Array – PGx - Star allele annotate

GRCh38

PRSbooster_20083382_A

v1.0, v1.1

DRAGEN Array – Genotyping

GRCh37

EPIC-8v1-0_B5

v1.0

DRAGEN Array – Methylation - QC

GRCh38

EPIC-8v2-0_A2

v1.0

DRAGEN Array – Methylation - QC

GRCh38

MSA-48v1-0_20102838_A1

v1.0

DRAGEN Array – Methylation - QC

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

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

Outputs

Per sample:

Per analysis batch:

Cost

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

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

Outputs

Per sample:

Per analysis batch:

Cost

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

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

Outputs

Per sample:

Per analysis batch:

Cost

Local: Per sample analysis.

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

Inputs

Outputs

Cost

PreviousWelcome to DRAGEN ArrayNextDRAGEN Array Cloud Analysis

Last updated 7 months ago

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Any human Infinium genotyping array including custom and semi-custom to create a SNV VCF output. Illumina provides 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.

•

• [may be pre-setup on cloud]

• [may be pre-setup on cloud]

• [pre-setup on cloud]

• [optional on cloud and local]

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• [optional on cloud and local]

• [optional on cloud and local]

•

• [cloud only]

• [cloud only]

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Local: No cost download from .

Cloud: to analyze and store data as needed.

Check Product & Analysis Compatibility here

See for further detail.

•

• [may be pre-setup on cloud]

• [may be pre-setup on cloud]

• [pre-setup on cloud]

• [pre-setup on cloud]

• [optional on cloud and local]

•

• [optional on local]

• [optional on local]

•

• [optional on local]

•

•

•

•

Local: No cost download from .

Cloud: to analyze and store data as needed.

Check Product & Analysis Compatibility here

See for further detail.

•

• [may be pre-setup on cloud]

• [may be pre-setup on cloud]

• [pre-setup on cloud]

• [pre-setup on cloud]

• [pre-setup on cloud]

• [optional on cloud and local]

•

• [optional on local]

• [optional on local]

•

• [optional on local]

•

•

•

•

•

•

Cloud: Per sample analysis. to store data as needed.

Visit the to learn more.

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 . A maximum of 1152 samples are supported, when sample sheet is used.

• [from iScan instrument] • [may be pre-setup on cloud] • [optional on cloud]

Per sample: • • Per analysis batch: • • • • •

Cloud: to analyze and store data as needed.

Illumina Support Site
iCredits
Illumina Support Site
iCredits
iCredits
Illumina Product Page
iCredits
Product & Analysis Compatibility
Product & Analysis Compatibility
Genome FASTA Files
IDAT(s)
Manifest Files
Cluster File
Genome FASTA Files
Sample Sheet
IDAT(s)
Manifest Files
Cluster File
Genome FASTA Files
CN Model File
Sample Sheet
IDAT(s)
Manifest Files
Cluster File
Genome FASTA Files
CN Model File
PGx Database File
Sample Sheet
IDAT(s)
Manifest Files
IDAT Sample Sheet
Pharmacogenomic Analysis for semi-custom arrays
Pharmacogenomic Analysis for semi-custom arrays
DRAGEN Array Methylation QC
with known limitations
Genotype Call (GTC) File
SNV VCF File
TBI Index File
Genotype Summary Files
Final Report
Locus Summary
Warning/Error Messages
Genotype Call (GTC) File
SNV VCF File
TBI Index File
CNV VCF File
BedGraph File
Genotype Summary Files
CN Summary File
Copy Number Batch File
Warning/Error Messages
Genotype Call (GTC) File
SNV VCF File
TBI Index File
CNV VCF File
BedGraph File
Star Allele JSON File
Star Allele CSV File
Genotype Summary Files
CN Summary File
Copy Number Batch File
Warning/Error Messages
Methylation Control Probe Output File
Methylation CG Output File
Methylation Sample QC Summary Files
Methylation Sample QC Summary Plots
Methylation Principal Component Summary
Methylation Manifest Files
Methylation Logs and Error Files