Questions tagged [gwas]
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84
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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
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, ...
- 1,042
6
votes
1
answer
457
views
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
6
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0
answers
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making my own population allele frequency table for input to IADMIX from Gnomad data (population admixture)? [closed]
Hi I'm a first time user of IADMIX. I tested on one known Finnish sample from the 1000Genome project using the softwares provided frequency table hapmap3.8populations.hg19.freqs and the prediction is ...
- 61
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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
5
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3
answers
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
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What does PCA mean on GWAS
I understand what GWAS is and I'm able to perform certain tests with the p-values, etc. But what I am having a hard time wrapping my head around is what PCA on GWAS means.
So let's say I have 100,000 ...
- 341
5
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answer
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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1
answer
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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
4
votes
1
answer
158
views
LD Score Regression Derivation hard to follow
I am trying to understand the derivations from Sullivan et al. (2015) in the Supplementary Material. There, it is mentioned in the first page that the least squares estimate of the j-th SNP effect, ...
4
votes
1
answer
177
views
How is the odds ratio of disease risk conferred by a 1-standard deviation increase in PRS calculated?
One standard deviation from the mean is commonly used to calculate a polygenic risk score for GWAS, e.g. human genetic disease.
Why is this a common metric, for example why not 2-SD or 1.96 SD as in ...
- 167
3
votes
2
answers
99
views
Summary statistics version problem
I am learning GWAS study and PRS for predicting disease. I was aligning my sequencing data with GRCH38 reference panel. However, in the PRS analysis step, I found that most of the summary statistics ...
- 315
3
votes
1
answer
3k
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What does liability mean in GWAS heritability?
I am reading about GWAS in heritability. They usually say to calculate heritability on a liability scale but after searching for this word "liability", I still don't understand clearly what does ...
- 55
3
votes
2
answers
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Can an alternate allele be more common than a reference allele?
I'm trying to analyze data from a genotype-phenotype association study. The genotype data is stored in csv files that record for each variant site and each subject, the alleles that the subject has at ...
- 33
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votes
1
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233
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GWAS, MWAS, EWAS: what are the (in)dependent variables?
I started reading some papers on X-wide association studies, where X can be metabolome, epigenome, etc... The authors usually describe which are the dependent and which are the independent variables ...
- 411