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genepi / imputationserver

Michigan Imputation Server: A new web-based service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity
https://imputationserver.sph.umich.edu/
GNU Affero General Public License v3.0
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Imputation failed due to strand flip errors #131

Open ebrigos opened 8 months ago

ebrigos commented 8 months ago

I am trying to impute though TOPMed web server. However, imputation cannot start because it complains about more than 10000 obvious strand flips. How should I fix this problem with my dataset? I know the steps but I would need access to the reference panel topmed-r3@1.0.0 (hg38). Thank you!

ebrigos commented 8 months ago

I just saw that in the results section there is a file with the snps excluded, the reason and the correction. I will use this to adapt my dataset to the reference panel.