Problems to extract a SNP list from .ped and .map files

Question

[saual.maria]

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

Answer 1

[saual.maria]

I have already fixed the problem... I was working with plink version 1.07 but the version 1.9 allows to set the number of chromosomes (that was the problem, by default plink assumes data are from humans). Therefore by adding --chr-set numberofchromosomes the problem is solved