I am currently facing a challenge with data I obtained from Illumina GSA 2.0 GWAS chip. The data format is .IDAT, which I am not very conversant with. I usually work with Affymetrix .CEL files. I have been able to call the genotypes from the IDAT files and converted it to Plink binary format. The problem is that the .fam file has missing phenotypes (-9) for all the samples. I have tried several tools, but they all seem not to be working. I have tried bcftools +gtc2vcf (https://github.com/freeseek/gtc2vcf#identifying-chip-type-for-idat-and-cel-files) and a Python script (https://github.com/Illumina/GTCtoVCF), which all did not work.

Is there a way I can impute the phenotypes (case/control) in plink? The available file types for each sample batch are SDF, CFG, IDAT and XML. I am unsure where the phenotype information is stored. Many thanks in advance.