Dear all. I want to remove a list of SNPs from my .ped and .map files. I have seen that plink has these instructions --exclude and --extract, that remove SNPs in the first case or create a new file with the SNPs you want to keep in the second case. Both would help me.

I execute the instruction:

plink --file myfile --extract mySNPlist.txt --recode --out newfile

(or the same in the opposite way)

plink --file myfile --exclude mySNPlist2.txt --recode --out newfile

and it works in both cases BUT when I open the new map file, although the number of SNPs is correct, it set many SNPs to 0 in the column corresponding to chromosome and I don't understand why, as the SNP list I provide only includes mapped SNPs.

Could you please help me with this? Thank you in advance. María