I am working with BGEN imputed files at Bulk/Imputation/UKB imputation from genotype.
Is there any way to know if a given variant in the BGEN file has been imputed or directly sequenced?
I am using Hail to process those files, so ideally using Hail.
Thank you
Thank you for the answer @Ondrej Klempir? ! I am not working with any particular field, I directly using the genetic variants to conduct some downstream analyses with them. And what I would like to know is how to differentiate a variant present in the BGEN file that has been directly sequenced from a variant that has been imputed (regardless of the imputation method). So far I can't see any "flag" in the bgen file that specifies if a given variant for a particular sample has been directly genotyped or imputed.
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I would check Bulk/Imputation/UKB imputation from genotype in terms of which field id you work with. Later, I would go to https://biobank.ndph.ox.ac.uk/showcase/search.cgi and search relevant field id. You will likely find all the details about the method there, e.g. https://biobank.ndph.ox.ac.uk/showcase/refer.cgi?id=10510
Thank you for the answer @Ondrej Klempir? ! I am not working with any particular field, I directly using the genetic variants to conduct some downstream analyses with them. And what I would like to know is how to differentiate a variant present in the BGEN file that has been directly sequenced from a variant that has been imputed (regardless of the imputation method). So far I can't see any "flag" in the bgen file that specifies if a given variant for a particular sample has been directly genotyped or imputed.
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