All Questions
4
questions
1
vote
0
answers
29
views
How to chose values for QC for a GWAS?
I am running a GWAS on a large dataset. I am using the H3aBioNet QC workflow (https://github.com/h3abionet/h3agwas/blob/master/qc/README.md).
I have run the QC on initial parameters:
MAF < 0.01
...
1
vote
1
answer
797
views
Plink error: --check-sex/--impute-sex requires at least one polymorphic X chromosome locus
I am running an analysis in plink.
This is my first attempt at a QC and I keep encountering the same message when I try to go through with my sex check. I've done the SNP missingness step, it's this ...
- 67
1
vote
0
answers
85
views
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
6
votes
1
answer
214
views
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, ...
- 1,042