Imputation output from TOPMED server

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3.8 years ago

mel22 ▴ 100

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 : )

The output of the imputation does it contain typed and untyped SNPs ?
If yes how to know the typed ones ?
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 !

SNP imputation TOPMED • 1.9k views

ADD COMMENT • link updated 3.8 years ago by zx8754 11k • written 3.8 years ago by mel22 ▴ 100

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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.