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Array Genotyping Conversion Tool

The AGCT (Array Genotyping Conversion Tool) pipeline consists of only 1 step: 1: Convert IDAT to GTC Format

This step takes IDAT files (Illumina SNP array scan Files) and converts them to GTC Format.
For this to happen, a reference file (in .egt format) to normalize the data is needed and also the manifest file (in .bpm format) is needed.
The bpm file contains information about which probes lie on the array platform.

After this conversion the array data can be converted to .txt files using the GAP pipeline.
These .GTC files can also be converted by using the Python library BeadArrayFiles.

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