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pjgreer / ukb-rap-tools

Scripts and workflows for use analyzing UK Biobank data from the DNANexus Research Analysis Platform
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liftover #11

Closed TrumanZYX closed 1 year ago

TrumanZYX commented 1 year ago

Dear, Thanks for your work. Thanks for your help.

pjgreer commented 1 year ago

If you want to combine imputed data with WES data, I would recommend using the new imputed data field 21007. This is imputed against the TOPMED reference panel and is already in GRCH38.

More info on the new data field here: https://biobank.ndph.ox.ac.uk/showcase/field.cgi?id=21007

I have not used it yet, but it should work well.

pjgreer commented 1 year ago

You may need to check the UKB RAP for updates.

See here for the TOPMED release: https://community.dnanexus.com/s/question/0D5t000004DDMDcCAP/new-data-release-genomics-england-and-topmed-imputation-data and here for some additional tips https://community.dnanexus.com/s/question/0D5t000004SBxtyCAD/potential-issues-with-imputed-data

see this page for how to update the data: https://dnanexus.gitbook.io/uk-biobank-rap/getting-started/updating-dispensed-data

You should be able to see the data using the dx ls command: dx ls "Bulk/Imputation/Imputation\ from\ genotype\ (TOPmed)/*.bgen"