Axiom Genotyping Analysis Software
May 2017
Axiom Analysis Suite (AXAS) is free to download from the ThermoFisher website at:
The Axiom Genotyping Analysis Guide and Axiom Analysis Suite Quick Reference Card are available to download at:
When your arrays have been processed, you will receive array intensity (CEL) files for the arrays corresponding to each of your DNA samples.
In addition to the CEL files and AXAS software, you will also need the Axiom analysis library files specific for the array type on your PC.
Chapter 7 of the Data Analysis Guide has detailed instructions for completing Best Practice Analysis (Chapter 3) of Axiom Intensity files (CEL) files using the Axiom Analysis Suite.
For the analysis Mode, select Best Practices Workflow, which will automatically perform Sample QC prior to running the genotype clustering, followed by AxiomGT1 genotyping of the passing samples, and finally SNPolisher classification, to generate the recommended SNP list based on SNP cluster characteristics.
Affymetrix Power Tools (APT)
To coincide with the release of Axiom Analysis Suite, there are new releases of the Affymetrix command line software, Affymetrix Power Tools (APT) and the SNPolisher R Library for advanced users.
APT1.18and above includes a new workflow specifically for genotyping Axiom arrays, apt-genotype-axiom, which is used instead of the original workflow, apt-probeset-genotype.
APT1.18 also includes the SNPolisher analysis applications: ps-metrics, ps-classification, ps-classification-supplemental and otv-caller.
So now it is only necessary to use the SNPolisher R library for the ps-visualization step, to generate the SNP cluster plots.
There are two additional applications applicable to Axiom arrays where appropriate:
Axiom® CNV Summary Tools Software
The Axiom CNV summary tools use intensity and genotypes to calculate log2 ratios and B allele frequencies from genotyping data. Also included in the Axiom CNV Summary Tools Software package is Axiom CNV Viewer.
When this is installed on a PC along with Axiom Analysis Suite, the Axiom CNV Tool can be accessed by clicking on the External Tools tab.
Note: CNV analysis is not applicable to all Axiom array types.
Axiom™ HLA Analysis
With Axiom HLA Analysis 1.1, you will now be able to produce accurate HLA types from any Axiom Human genotyping data containing high-quality genotypes of a select number of predetermined markers.
Axiom HLA Analysis 1.1 requires the genotype calls in .VCF format, which is one of the SNP export options available in AXAS.