Questions tagged [gwas]
The gwas tag has no usage guidance.
84
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Assuming that we have the following SNP and phenotype data, is the SNP significantly associated with the phenotype?
So if I attempt this question using their method I put the data of genotype and phenotype into a data frame in R then use lm() to do linear regression and ...
- 33
3
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1
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What are the differences between GWAS and QTL mapping? [closed]
What are the differences between the two methods?
What advantages does one have over the other, and what are their limitations relative to one another?
- 69
6
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2
answers
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PLINK clump behavior on missing SNPs?
I have a long list of autoimmune-associated SNPs, and I want to boil it down so that I get one SNP representing each LD block. I chose to use PLINK's --clump option for this. I'm roughly following ...
- 380
5
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1
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Adjusting phenotypes by regressing out covariates
I'm trying to use the bfGWAS tool, which analyses GWAS data and integrates functional annotations to identify casual SNPs (paper and
github). In the user manual, it states:
We recommend first ...
- 153
5
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1
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1k
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How to deal with correlated SNPs in GWAS?
I have population SNP data in VCF format, and I found that some SNPs have a great similarity across samples(> 99%). For example:
...
- 325
5
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3
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Is there any difference between SNPs 'AG' and 'GA' in association analyses?
I am using plink to check the association between a phenotype and the SNPs of a gene. plink says the phenotype is significantly associated with a SNP on that gene, and when I check the SNP alleles, ...
- 305
6
votes
1
answer
457
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Where can I find a GWAS data set about genotypes and phenotypes for Zebrafish and rice?
My goal is to work on GWAS method development as a research project. However, human genome data are usually confidential because of the identification problem, so it's very hard to get them. (...
- 521
5
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3
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216
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Where can I find a database that has phenotype information together with associated SNPs?
I have been searching for a long time and the furthest I got is some database with the functional description for genes. Then, I have to parse these descriptions manually to figure out the association....
- 521
6
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1
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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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