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Format of SNP RS# in plink formatted .map

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.

ped snp
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updated by Ram Ram • written by genomics Newbie • genomics Newbie

1 answer

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.

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written by WouterDeCoster WouterDeCoster

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