What Is A Snp Manifest And What Is A Snp Cluster File?

Question

[Click downvote]

And what are what are their uses?

I do not know if these are general terms or only used in the context of GenomeStudio analysis....

Answer 1

[zx8754]

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.

[ektaj.1jain]

Dear zx8754,

In your response you mention that "customers may generate their own cluster file". I have been looking to generate my own cluster files for genome studio but cannot seem to find how to do this. Would you please be able to tell me how and or point me to material so that I am in the right direction?
Many thanks,

EJ

Answer 2

[John]

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.