I m trying to analyses one of the illumina beadcheap. So the protocol I followed is process the data including idat,manifest and cluster file in genome studio, export them as plink format and the downstream using plink tool.

This is what I'm using

./plink_19.exe --bfile small_subset_binary --maf 0.01 --geno 0.05 --mind 0.1 --hwe 1e-6 --make-bed --out  small_sub_clean 

Now two rsid which we are expecting to be present in the final vcf file is not there its present in the fill data table.

What can be the reason ? or am I doing something incorrect