I have Illumina MEGAEx Genotyping. idat files and I need to conduct QCing for the same. I am interested in conduction QC on SNPs located in a haploid genome. But, when I spoke to the person who did this Genotyping hybridization, he says that they did not capture the gender details of the sample. Now we don't have any info regarding the gender of the samples, this data was from 2017. I want to make the best use of it, it would be great if you can let me know how to conduct QC on SNPs located in a haploid genome in GenomeStudio in this case.
I would be very happy if you guys can help me.
Thanks a lot for your kind help.