It is now recommended to use the fully supported Illumina solution DRAGEN Array to convert IDAT to VCF files

./main.sh -h

A simple program to covert .idat files to plink format files.
Options:
-b     A path to .bpm manifest.
-s     A path to .csv manifest.
-c     A path to cluster .egt.
-i     A path idat files directory.
-o     A path to gtc output directory.
-g     A path to reference genome .fasta.
-p     A prefix for output file.
-h     Show this help and exit

In order to run the scripts, you have to have following files:

• Manifest file from your microarray experiment. This file can be found in Illumina website. For instance, Infinium ASA Screening Array. Download both .csv and .bpm
• Cluster file in format .egt from your microarray experiment. For instance, Infinium ASA Screening Array
• Reference genome in .fasta format. The reference build version should follow your manifest and cluster files. Which human reference genome to use

Also, you have to install these following programs and move the binaries to your $PATH:

• IAAP Genotyping Command Line Interface (CLI)
• bcftools and gtc2vcf
• PLINK
• BeadArrayFiles