Question: Format of SNP RS# in plink formatted .map
gravatar for genomics Newbie
20 months ago by
genomics Newbie20 wrote:

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.

snp .ped • 694 views
ADD COMMENTlink modified 20 months ago by WouterDeCoster41k • written 20 months ago by genomics Newbie20
gravatar for WouterDeCoster
20 months ago by
WouterDeCoster41k wrote:

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.

ADD COMMENTlink written 20 months ago by WouterDeCoster41k
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