Question: QC after Imputation
gravatar for Mir09
3.4 years ago by
United States
Mir090 wrote:

If I just want to use 3 snps from an imputed dataset, where 2 were imputed snps. Would I need to run basic qc procedures again of the merged imputed dataset (snp & sample call rates, hwe, ibd, pca), if the snp passed pre-imputation qc and post imputation info score filter?  I know that for gwas types of studies, it is recommended to run post-imputation qc.  However, if one is interested in a small subset, say even 1 chromosome, can you just run these sanitary checks on the snps/chr you're testing?

Thank you so much for your input.

myposts qc gwas • 2.6k views
ADD COMMENTlink modified 3.4 years ago by SES8.1k • written 3.4 years ago by Mir090

Relevant post: How To Analyze Imputed Gwas Data

ADD REPLYlink written 3.3 years ago by zx87546.8k
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