Question: QC after Imputation
gravatar for Mir09
3.9 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 • 2.9k views
ADD COMMENTlink modified 3.9 years ago by SES8.2k • written 3.9 years ago by Mir090

Relevant post: How To Analyze Imputed Gwas Data

ADD REPLYlink written 3.9 years ago by zx87548.2k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1114 users visited in the last hour