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=== '''Shall I apply QC before or after imputation? If so, how? '''  ===

=== '''Shall I apply QC before or after imputation? If so, how? '''  ===

A: Yes. We strongly recommend QC both before and after imputation. Before imputation, we recommend the standard battery of QC filters including HWE, MAF (recommended cutoff is 1% for genotyping-based GWAS), completeness, Mendelian inconsistency etc. Post-imputation, we recommend Rsq 0.3 (which removes >70% of poorly-imputed SNPs at the cost of <0.5% well-imputed SNPs) and MAF of 1%.  

We strongly recommend QC both before and after imputation. Before imputation, we recommend the standard battery of QC filters including HWE, MAF (recommended cutoff is 1% for genotyping-based GWAS), completeness, Mendelian inconsistency etc. Post-imputation, we recommend Rsq 0.3 (which removes >70% of poorly-imputed SNPs at the cost of <0.5% well-imputed SNPs) and MAF of 1%.  

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=== '''How do I get reference files for an region of interest? '''  ===

=== '''How do I get reference files for an region of interest? '''  ===