Hi,

   After getting a genotype, scan annotation, SNP annotation files from Illumina in R using GWASTools, I was checking for table(diag.geno$snp.chk). Although the SNP ID matched in geno.file and SNP annotation file  table(diag.geno$snp.chk) gives 0 for all my samples. The diag.geno gives the following output

missg                list[151]                    list of length 151

snp.chk             double [151]            0 0 0 0 0 0 .....

chk                    logical                      NA NA NA NA NA ....

I am not sure what I am missing, any help is appreciated. 

Thank you, 

PD