Question: Imputation output from TOPMED server
0
gravatar for melania 2282
6 days ago by
melania 228290
melania 228290 wrote:

Hello,

As beginner and it's my first imputation, I have few questions about TOPMED imputation server please any one used to this type of imputation server could help : )

  1. The output of the imputation does it contain typed and untyped SNPs ?
  2. If yes how to know the typed ones ?
  3. When a filter based on r2 is used, does it deleted the typed SNP from the VCF as they don't have an r2 value ?

Thank you very much !

topmed snp imputation • 56 views
ADD COMMENTlink modified 6 days ago by zx87549.3k • written 6 days ago by melania 228290

1- The output of the imputation does it contain typed and untyped SNPs ?

  • This question is worded a little strange, but should contain both if I understand your ask right. open the "info" file that comes with the download to see which sites were typed only (not in the reference panel) or typed and imputed. Check the header of the vcf for more definition on the terminology.

3- When a filter based on r2 is used, does it deleted the typed SNP from the VCF as they don't have an r2 value ?

  • You should be able to use grep and the info file to figure this one out on your own, a hint is to look at the definitions in the header and my answer to question 1.
ADD REPLYlink modified 6 days ago • written 6 days ago by curious320
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