I am merging data sets, and the SNP IDs between the two are inconsistent, likely because Affx numbers changed between annotations. For example, merging SNP lists (in R) based on SNP ID loses me ~50,000 SNPs, but merging based on coordinate will only lose me ~10,000 SNPs (i.e., 545,956 sites vs. 585,413 sites).
If I have a command as such
plink --file data1 --merge data2.ped data2.map --recode --out merge
What do I do to tell Plink to ignore the SNP IDs from data2 and merge based on coordinate, not SNP ID?