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](https://help.connected.illumina.com/dragen-array/dragen-array-v1.0/product-guides/input-files#toc150786139) 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:
• 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 | 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:
• SNV VCF File \[optional on local]
• TBI Index File \[optional on local]
• BedGraph File \[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 | 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:
• SNV VCF File \[optional on local]
• TBI Index File \[optional on local]
• BedGraph File \[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 – 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](https://help.connected.illumina.com/dragen-array/dragen-array-v1.0/product-guides/dragen-array-cloud-analysis#dragen-array-methylation-qc). A maximum of 1152 samples are supported, [with known limitations](https://help.connected.illumina.com/dragen-array/dragen-array-v1.0/product-guides/dragen-array-cloud-analysis#known-issues) 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]
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