From illumina Questions & Answers

What is a beadpool manifest?

Also referred to as a SNP Manifest, this is a file containing the SNP-to-beadtype mapping, as well as all SNP annotations. For the Infinium assay, this is a *.bpm file in binary format.

What is a cluster file?

The cluster file contains the mean (R) and standard deviation (theta) of the cluster positions, in normalized coordinates, for every genotype, for every SNP. The cluster file also includes cluster score information, as well as the allele frequencies from the training set used to generate the cluster file. A cluster file is required for KaryoStudio. Illumina provides a standard cluster file for each product. Alternatively, customers may generate their own cluster file.

In simpler terms SNP manifest files consists of marker information in the array.

(1) The provider will send you this file and use this file with other files to create genomestudio file.

(2) You can then maker cluster calls manually or using built in clustering algorithm or both.

(3) Once you done with clustering in genomestudio, you can create a report with genotypes.

(4) You can also output cluster file, which can be used for clustering in future without needing to go through step (2) again, Thus cluster file includes information about clusters for all SNPs.