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Tagged with gwas imputation
4
questions
2
votes
0
answers
55
views
Publicly available population specific reference panels
The publicly available reference panel for GWAS analysis is the 1000 genomes reference panel. The reference panel consists of several populations. However, I am searching for a population-specific ...
- 315
1
vote
0
answers
85
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What is the best QC to do on imputed UK Biobank data?
I am receiving imputed data from UK Biobank to conduct a GWAS on. Previously I have carried out GWAS on genotype data, which I have QC'd for missingness per individual and per SNP, sex discrepancy, ...
- 155
3
votes
2
answers
2k
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How to filter info score post-imputation?
this is a very basic question, but I cannot find it explicitly stated anywhere: When exactly should I filter the info scores after imputation?
I did imputation in Impute2 and am planning on using ...
- 31
6
votes
1
answer
214
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Filtering imputed GWAS SNPs based on a MAF difference of 10%
There are many posts on the web regarding QC steps pre and post-imputation.
Does applying below (new?) 10% MAF difference rule make sense, pitfalls?
Here is the process:
Get MAF for imputed set, ...
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