Manifest Files and Cluster Files

For each BeadChip, the software requires access to a manifest file and cluster file. Each manifest and cluster file is unique to a BeadChip type. Make sure that you use cluster files that include NS550 in the file name. These files are compatible with the NextSeq system.

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Manifest file—Manifest files describe the SNP or probe content on a BeadChip. Manifest files use the BPM file format.

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Cluster files—Cluster files describe the cluster positions for the Illumina genotyping array and are used when analyzing data to make the genotype call. Cluster files use the EGT file format.

The location of the files is specified on the BeadChip Scan Configuration screen. From the NCS Home screen, select Manage Instrument, System Configuration, and then BeadChip Scan Configuration.

When the NextSeq 550 instrument is installed, the Illumina representative downloads these files and specifies the path in the control software. There is no need to change these files except in the case of loss or if a new version is available. For more information, see Replace Manifest Files and Cluster Files.