DRAGEN Array Applications
The following Types of Analysis are currently supported by DRAGEN Array:
DRAGEN Array – Genotyping and QC
DRAGEN Array – PGx – CNV calling
DRAGEN Array – PGx – Star allele annotation
DRAGEN Array – Cytogenetics analysis
DRAGEN Array - Cytogenetics analysis + Emedgene interpretation
DRAGEN Array – Methylation QC
Product & Analysis Compatibility
These products/beadchips have been verified to be compatible with the analyses below.
To make the compatibility matrix easier to review, the tables are split by product category and ordered by product group, product, tested manifest, and analysis type.
Notes:
The Manifest column lists the tested BPM/CSV product file revision.
Some historical manifest rows from the previous compatibility table were intentionally folded into the newer tested manifest revisions listed here. See the release notes when version-specific legacy manifest support details are needed.
The cloud and local version columns indicate the version where support was introduced and later retained, unless noted otherwise.
Historical PGx manifest transitions for older releases are described in the release notes.
Genotyping, PGx, and Cytogenetics Products
Genotyping
CGA
CGA-24v1-0_A1
Genotyping
v1.1, v1.4
v1.0+
GRCh37, GRCh38
Genotyping
JSA
JSA-24v1-0_B2
Genotyping
v1.1, v1.4
v1.0+
GRCh37, GRCh38
PGx
GCRA-ePGx
Genotyping; PGx – CNV calling; PGx – Star allele annotation
v1.1+
v1.1+
GRCh38
Introduced with EX PGx support
PGx
GDA-ePGx
Genotyping; PGx – CNV calling; PGx – Star allele annotation
v1.1+
v1.1+
GRCh38
Current tested G-series manifest
PGx
GSAv4-ePGx
Genotyping; PGx – CNV calling; PGx – Star allele annotation
v1.1+
v1.1+
GRCh38
Introduced with EX PGx support
Cytogenetics
GDA Cyto
Cytogenetics analysis + Emedgene interpretation
v1.2+
N/A
GRCh37, GRCh38
Cloud only analysis type
Cytogenetics
GSA Cyto
Cytogenetics analysis + Emedgene interpretation
v1.2+
N/A
GRCh37, GRCh38
Cloud only analysis type
Cytogenetics
CytoSNP-850K iScan
Cytogenetics analysis
v1.2+
v1.2+
GRCh37, GRCh38
Cytogenetics
CytoSNP-850K iScan
Cytogenetics analysis + Emedgene interpretation
v1.2+
N/A
GRCh37, GRCh38
Cloud only analysis type
Cytogenetics
CytoSNP-850K NS550
Cytogenetics analysis
v1.3+
v1.3+
GRCh37, GRCh38
Cytogenetics
CytoSNP-850K NS550
Cytogenetics analysis + Emedgene interpretation
v1.3+
N/A
GRCh37, GRCh38
Cloud only analysis type
Methylation Products
EPIC-Xtra
EPIC-Xtra_GS_20144570_A1.csv
Methylation – QC
v1.0
N/A
GRCh38
Custom methylation product.
DRAGEN Array – Genotyping and QC
Summary
Provides genotyping results and sample QC report for Infinium genotyping arrays. Non-human species are also supported for diploid organisms when a reference genome is provided.
Variant types detected
SNV
Indel
Sample minimum
1 sample
Arrays supported
Any Infinium genotyping array, including human (including custom and semi-custom) and non-human diploid species, 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; for non-human diploid species, a user-provided reference genome is required. DRAGEN Array Cloud offers additional output formats including Locus Summary and Final Report which are applicable for Infinium arrays for human and non-human diploid species.
Related Local Commands
genotype call
genotype gtc-to-vcf
qc call
qc report
Related Cloud Specifics
Select Type of Analysis DRAGEN Array – Genotyping and QC 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]
• QC Report Config File [pre-setup on cloud]
Outputs
Per sample:
• SNV VCF File [optional on cloud and local]
• TBI Index File [optional on cloud and local]
Per analysis batch:
• Final Report [cloud only]
• Locus Summary [cloud only]
Cost
Local: No cost download from Illumina Support Site.
Cloud: iCredits to analyze and store data as needed.
DRAGEN Array – PGx – CNV calling
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:
• SNV VCF File [optional on local]
• TBI Index File [optional on local]
• BedGraph Files [optional on local]
Per analysis batch:
Cost
Local: No cost download from Illumina Support Site.
Cloud: iCredits to analyze and store data as needed.
DRAGEN Array – PGx – Star Allele Annotation
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:
• SNV VCF File [optional on local]
• TBI Index File [optional on local]
• BedGraph Files [optional on local]
Per analysis batch:
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 – Cytogenetics analysis
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 – Cytogenetics analysis 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] • QC Report Config File [pre-setup on cloud]
• Cytogenetics Model File [pre-setup on cloud]
• Cytogenetics Database File [only necessary for local]
• 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 Annotation JSON File
• BedGraph Files [optional on local]
Per analysis batch:
Cost
Local: No cost download from Illumina Support Site.
Cloud: iCredits to analyze and store data as needed.
DRAGEN Array - Cytogenetics analysis + Emedgene interpretation
Summary
Provides cytogenetic genome-wide copy number and loss of heterozygosity calling. This analysis type integrates with Emedgene via Automatic Case Creation from ICA on cloud only.
Variant types detected
CNV
LOH
Sample minimum
Minimum of 1 sample.
Arrays supported
Check Product & Analysis Compatibility here Product & Analysis Compatibility
Related Local Commands
Not available on DRAGEN Array Local.
Related Cloud Specifics
Select Type of Analysis DRAGEN Array - Cytogenetics analysis + Emedgene interpretation from the dropdown. Max 1152 samples are supported.
Inputs
• IDAT(s)
• Manifest Files [may be pre-setup]
• Cluster File [may be pre-setup] • QC Report Config File [pre-setup on cloud]
• Cytogenetics Model File [may be pre-setup]
• Sample Sheet [optional]
Outputs
Per sample:
• Genotype Call (GTC) File [optional]
• SNV VCF File [optional]
• TBI Index File [optional for snv vcf]
• Cytogenetics Annotation JSON File
Per analysis batch:
DRAGEN Array – Methylation QC
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] • Sample Sheet [optional on cloud]
Outputs
Cost
Cloud: iCredits to analyze and store data as needed.
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