Questions tagged [gwas]
The gwas tag has no usage guidance.
84
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52
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Excess average estimated identical-by-descent in genotype data
(Cross-post with Biostars: https://www.biostars.org/p/470788/)
We have some genotype data that we are putting through quality control in PLINK 1.9. As part of this QC, we have limited the data to ...
- 133
2
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2
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74
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Loss of predictive power of polygenic risk score when dataset contains missing variants
I am trying to calculate polygenic risk scores (PRS) scores for a new dataset. This dataset does not have all the variants that the PRS score needs. The PRS score I am interested in has 40 variants, ...
- 21
1
vote
1
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70
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Apply trained PRS on another dataset
I am using PRSice to compute the PRS over a train set and want to use the coefficient used on the train set to apply it on another set which I will call the test set.
Once I compute the PRS I get a ...
- 113
0
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0
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222
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GWAS phenotype data format and preprocessing
I have a set of different phenotypes which I want to use for a GWAS analysis (general linear model). I have a couple of questions and uncertainty about the phenotype data input.
I have control and ...
- 147
1
vote
2
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263
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Interpreting GWAS results with different settings
I did a bunch of GWAS analysis (linear model without covariates) with applying different quality controls. How to choose the optimal settings when filtering for minor allele frequency (maf), Hardy-...
- 147
0
votes
1
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155
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Odds ratio and enrichment of SNPs in gene regions?
I did a QTL analysis with a panel of 7M SNPs, and want to analyze the enrichment of the significant qtl-SNPs in different genic regions (promoters, gene bodies, TFBS, etc.).
A straightforward way to ...
- 35
1
vote
1
answer
127
views
GWAS MAC filter Interpretation
I am performing a GWAS analysis and try to understand the influence of the minor allele count filter.Setting the filter to 1 % gave me this plot and I am confused about the same -log10 pvalues around ~...
- 147
1
vote
1
answer
228
views
Power calculation for GWAS/EWAS
I want to investigate, how much sample size i needed to obtain 80% power for GWAS/EWAS studies. Phynotype trait is discrete (not case/control) for human disease.
I wonder, does anyone has came across ...
- 61
1
vote
1
answer
2k
views
Convert VCF to genotype table
How can I convert a VCF file into a genotype table (SNP matrix)?
I have this format:
...
- 147
1
vote
0
answers
34
views
GWAS Rooted PCA analysis problem
I'm fairly new to plink software and wanted to get some additional practice after doing several tutorials. I obtained the data from this paper (I'm not using this paper's methods) to do some QC with ...
- 11
0
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2
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122
views
Should you filter GWAS hits with high standard error?
I'm trying to figure out if I should be filtering out GWAS hits that have high standard error and I'm not quite sure what to do. It seems like it might not matter, because the standard error is used ...
- 831
1
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2
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213
views
How to combine two Genome-wide Association Study (GWAS)? [closed]
I did a GWAS analysis in the past for antibiotic resistance of E. Coli and the results were interesting (matching the literature). I did a new GWAS analysis for some new samples, but the results are ...
- 107
0
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1
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122
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How to analyze co-occurrence of multiple SNPs?
I am interested in 20 different SNPs that all are either As or Gs, and they all occur on the same chromosome. How can I assess the co-occurrence of these SNPs? In other words, I want to know, if SNP1 ...
- 151
3
votes
1
answer
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
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70
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Question: How to simulate 100k samples having 40 million SNPs in a proportion of case:control=30:70?
Note: this question can also be found on Biostars
I need to perform a stress test in a GWAS tool and the duty demands a dataset (plink format) having 100 thousand samples, having 40 million SNPs in a ...
- 207