I converted 23andme raw snp data to vcf format for 750 individuals and all of them have same rsnpid's. Then I convert them to gds format using convertVcfGds(vcf, gdsfile) function in SNPRelate package. I need to merge all individual's gds files into one gds file and use it for hieararchical clustering. However, when it merges, after 17th individual I get "there is no common snp" error. I also try to merge the 1st,2nd,3rd individuals and number of common snps decrease after every individual.
What am I doing wrong?
Thank you so much