QC of UKB BGEN format data
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2.6 years ago
Salahuddin • 0

Hi , I have a question. While PRScoring with BGEN imputed UKB data in PRSice-2 program, I only did INFO, MAF and Geno filtering as QC. Is it enough QC steps for UKB imputed BGEN data? From 'Tutorial: a guide to performing polygenic risk score analyses'paper I see additional recommendation of QC. 'Genotyping rate >0.99' and 'Hardy-Weinberg Equilibrium P >1 × 10−6'. How to apply that while working with UKB BGEN data? And if not needed, can i get a reference to that. Thanks

QC BGEN UKB risk PRSice scoring • 770 views
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I think UK Biobank already provides QC of the data. You can check their help pages.

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