I am using Plink for GWAS studies. For the data cleaning step, when I am filtering for MAF (minor allele frequency), it is giving me some warnings such as -
"Plink is setting 111834 heterozygous haploid as missing"
From the following link, I found that it could be solved by "--split-x" command but I am finding difficulty to use it. https://www.cog-genomics.org/plink2/data#split_x
It would be great if anyone can give me an example command so, I could get an exact idea of its usage?
Thanks a lot.