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Filter types in the Michigan imputation server output

Hi all,

I have a question about understanding the two filter types from the Michigan imputation server output. The header of output illustrates the two types as 

##FILTER=<ID=GENOTYPED,Description="Marker was genotyped AND imputed">
##FILTER=<ID=GENOTYPED_ONLY,Description="Marker was genotyped but NOT imputed">

I'm confused about how the server classifies which SNP to be genotyped and which to be genotyped_only?

Thank you very much!

snp software error
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written by Sonya • Sonya

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