> For the complete documentation index, see [llms.txt](https://knowledge.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://knowledge.illumina.com/microarray/general/microarray-general-reference_material-list/000009546.md).

# At which stage in Microarray analysis does the Genome Build come into play?

The manifest file of each BeadChip lists all the positions that the BeadChip is supposed to assay - basically a list of all the SNPs in a genotyping BeadChip, or a list of all the methylation sites in a methylation BeadChip. It also lists which bead types on the BeadChip (Infinium I or II) is associated with each position. The manifest also contains the genomic information for each SNP or methylation site, ie, the chromosome and genomic location for each site being assayed. For human samples, for example, those coordinates are based on either Genome Build 37 or Genome build 38, depending on which manifest is applied. Users can check the Genome Build information in the column "Genome Build" (or "Genome\_Build)" of manifest files.

GenomeStudio merges the IDAT files that contain the intensity information with the manifest, associates all the intensities to their proper positions, and calculates assay results (genotypes or methylation states) for that position. For genotyping, users can choose either Build 37 or Build 38 - the name of the manifest will end with different numbers to differentiate manifests with coordinates based on Build 37 or on Build 38. The list of positions are exactly the same, it is only the added annotations which are different, and users can choose which one to apply to the IDATs. For methylation, the manifest contains coordinate information for both Build 37 and Build 38 - users choose which one to include in the report.

The same choice of manifest is afforded the user when generating GTC (genotype call) files. The GTC files will include the coordinate annotations based on which manifest was applied during GTC file creation.

Note that the manifest choice does not affect the calls made for the SNPs or methylation sites and only affects downstream applications inasmuch as those applications rely on the coordinates embedded in the GTC or GenomeStudio reports.

**Additional references:**

* [How to identify which Manifest and Cluster Files were used to generate a GTC File?](/microarray/general/microarray-general-troubleshooting-list/000001484.md)
* [Infinium genotyping manifest column headings](/microarray/general/microarray-general-reference_material-list/000001565.md)
* [Infinium MethylationEPIC v2.0 Manifest Column Headings](/microarray/general/microarray-general-reference_material-list/000009183.md)

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| *For any feedback or questions regarding this article (Illumina Knowledge Article #9546), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000009546%20-%20Microarray%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


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