Format of SNP RS# in plink formatted .map

Question

[genomics Newbie]

This is a newbie question. In my .map file (formatted by plink) I was expecting all RS numbers. However, many SNPs are named var_chrxx_yyyyy, where x is the chromosome number and yyyyy is the base pair position.

• Is this a correctly formatted SNP number?
• Do I need to remove these SNPs from both my .ped and my .map file?

Thank you.

Answer 1

[WouterDeCoster]

How did you get that map file? Plink probably got those identifiers from the vcf file.

rs numbers are identifiers as submitted in dbSNP. But not all variants have a rs number since not all are submitted in dbSNP. Therefore the var_chrxx_yyyyy notation is a fine alternative for variants lacking a rs number, and there is no reason to remove those.