Third-Party Support
Affymetrix Support
Golden Helix SNP & Variation Suite™ software is an Affymetrix GeneChip-compatible application with support for importing genotype and intensity data from Affymetrix GeneChip arrays and associated library and annotation (marker map) files for SNP and copy number analysis.
Below are tips and commonly accessed files that will help you get the most from your Affymetrix data.
Supported File Types
The following is not an exhaustive list and is subject to change. Please contact support for the most up-to-date information.
For SNP analysis, SVS supports the import of CHP files from the following arrays:
- Genome-Wide Human SNP Array 6.0
- Genome-Wide Human SNP Array 5.0
- Human Mapping 500K Array
- Human Mapping 100K Array
- Human Mapping 10K Array
- Axiom Array
For CNV analysis, SVS supports processing of CEL files from the following arrays to compute LogR values for copy number analysis:
- Genome-Wide Human SNP Array 6.0
- Genome-Wide Human SNP Array 5.0
- Human Mapping 500K Array
- Cytogenetics Whole-Genome 2.7M Array
For the above arrays, various Affymetrix tools can be used to process CEL files and compute LogR, B-Allele frequency, copy number state and other values. These can be imported through the support of CYCHP, CNT and CNCHP files. Additionally, SVS has a custom import script for the Molecular Inversion Probe (MIP) array: MIP CN Transformation Script
Tutorials
Read the following tutorial for step-by-step workflows on how to perform SNP and copy number analysis using Affymetrix arrays:
5.0 and 6.0 Marker Maps and Annotation Files
Affymetrix 5.0 and 6.0 annotation files come in two separate files, one containing SNP probes and the other copy number probes. In order to properly process and analyze 5.0 and 6.0 data for copy number analysis you need the set merged and imported into SVS.
If you are having trouble downloading the latest Affymetrix annotation files using the NetAffx service, you can download them here for the 5.0 and 6.0 arrays.
Note: These files may not always be up to date.
- For Affy 5.0 click the following link: Affy SNP5 Marker Map.dsm
- For Affy 6.0 click the following link: Affy SNP6 Marker Map.dsm
Library Files
If you are having trouble downloading the latest Affymetrix library files using the NetAffx service, you can download them here for the 5.0 and 6.0 arrays.
- For Affy 5.0 click the following link: GenomeWideSNP_5.Full.cdf
- For Affy 6.0 click the following link: GenomeWideSNP_6.Full.cdf
Illumina Support
Golden Helix SNP & Variation Suite™ software is part of the Illumina Connect network of tools for analyzing BeadArray data for both SNP and copy number analysis.
Below are tips and commonly accessed files that will help you get the most from your Illumina data.
Illumina BeadStudio Plug-ins
In collaboration with Illumina, the Golden Helix? team has developed a set of custom plug-ins to streamline the transfer of genotype, log ratio and bookmark files between Golden Helix's SNP & Variation Suite™ applications and Illumina's BeadStudio and GenomeStudio Data Analysis software programs.
| Illumina Software | Plug-In | Version | Documentation |
|---|---|---|---|
| Genome Studio | Golden Helix GenomeStudio DSF Plugin-4.1.exe | 4.1 |
|
| BeadStudio | Golden Helix BeadStudio DSF Plugin-4.1.exe | 4.1 |
|