New Data Release: Genomics England and TOPMed Imputation Data
The latest data release is now available on RAP. This release includes imputed genotyping data using the Genomics England reference panel and TOPMed reference panel. Researchers can use these additions to the dataset for GWAS or other common variant study in addition to the originally released imputed data by UKB (22828).
Platform users can use the refresh feature on RAP to access the data in their projects. This refresh feature allows the researchers to use the existing projects with all the pipeline and logs without having to create a new project.
The RAP documentation has been updated with the release.
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If anyone is interested in this data, please also check out this thread. We add some note regarding some data format issue and solution to it. https://community.dnanexus.com/s/question/0D5t000004CaydsCAB/have-questions-about-the-gel-or-topmed-impute-data-release-ask-them-here
Where I can find the imputation quality information for TOPMed data. There is resource 1967 but when I download it it is on HG19 which makes me think that it is related to older imputation datasets as TOPMed is on HG38.
We have used UKBB TOPMed imputed data as control set for GWAS of different diseases and there were a lot of genome-wide significant hits across the genome which we did not expect as out sample sizes were small. We compared the genome-wide significant hits for different diseases and realized that many of them overlap. We checked MAF in our case sets and UKBB controls with dbSNP, and MAF in our cases are mostly similar to dbSNP but UKBB MAFs are very different. Therefore, we were wondering what is causing these big differences in UKBB AFs.
Please start a new thread for this discussion, to make it more visible.
(This thread was copied over from the old forum.)
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