# Questions tagged [gwas]

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1 vote
25 views

### How to interpret a negative beta within a binary GWAS?

I have run a GWAS on a binary trait - "Are you following a carnivore diet?" - so the cases are individuals who follow this diet, and the controls are individuals who do not follow this diet. ...
• 145
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### 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 ...
1 vote
56 views

### Why is the p-value significance threshold for HLA association tests $5*10^{-8}$? [closed]

Typically, a p-value of $p<=5*10^{-8}$ is used for genome-wide association testing, as there are roughly $1/p$ independent LD blocks in the human genome, so it correct for multiple testing across ...
• 1,194
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### Regression plot of a continuous trait - is there a binary equivalent?

Within the GWAS wikipedia page, you can view the following plot: "Illustration of a simulated genotype by phenotype regression for a single SNP. Each dot represents an individual. A GWAS of a ...
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### LD Clumping vs. Conditional Analysis for independent associations

I am working with some GWAS summary statistics. My ultimate goal is to extract variants to use as instrument variables for Mendelian Randomization analysis, which requires me to find SNPs that are ...
• 109
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### Applying GWAS summary statistics obtained from European people to other ethnicities (south Asian, African, east Asian, etc)

I was working with on a GWAS study of height using this tutorial. However, most of the summary statistics are obtained from European individuals. Is there any way we could reuse the summary statistics ...
26 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 ...
103 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, ...
68 views

### Polygenic Risk Scores

I have run a GWAS and used PRSice (https://www.prsice.info/) to calculate polygenic risk scores on the data collected from the GWAS. I need to check whether alcohol dependence can predict gambling ...
1 vote
24 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
150 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 ...
22 views

### Publicly available genotype / phenotype dataset?

I'm looking for publicly available genotype data (eg. 1000 Genomes or HapMap) that also has associated phenotypes (any traits). I'm wanting to use it as a test run for a GWAS pipeline. Does anyone ...
65 views

### HG19 Position meaning

I am looking at genomic data (HG19). I have many SNPs, their chromosomes and positions. I want to look at certain SNP (suppose its chromosome is 1 and position 77,226,919), and extract all SNPs in ...
• 231
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### Polygenic scores in diabetic individuals across UKBB

I am calculating PRS for a binary trait (T2D) across UKBB individuals. I am using external GWAS from PRS catalog in order to acquire weights for the base file. I have noticed the weights are given in ...
• 21
1 vote
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### How to convert the chromosome position for insertions/deletions to rsIDs in a GWAS summary statistics?

I am trying to convert chromosome positions to rsIDs of a GWAS summary statistics file. I used bedtools intersect to merge the reference genome GRCh37 and the ...
• 11
1 vote
36 views

### Gwas analysis studies using the result of differential analysis

I want to do a GWAS analysis using the differentially expressed genes that I got from a differential analysis. The purpose is the identification of biomarkers. It's my first time using GWAS, can you ...
• 63
1 vote
27 views

### Reason for linear effects dominating the difference in a quantitative trait between individual genomes

I'm an interested layman reading the paper https://arxiv.org/pdf/1408.3421.pdf (Hsu, Stephen, On the genetic architecture of intelligence and other quantitative traits, 2014). I'm trying to understand ...
• 11
1 vote
40 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, ...
• 145
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### Association test to get p values and OR in plink2, and file input format

Are there any commands for association testing in plink2 which will output p-value and OR in the resulting output file? If so, what kind of file input do I need to use for such commands...a vcf.gz ...
1 vote
34 views

### GWAS : input files for rrBLUP package in R

I want to do a verification of the result of an RNAseq analysis of human cancer samples by GWAS, I want to use rrBLUP package in R, so I need three input file genotype, phenotype and mapping file, so ...
• 63
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### Question about the practical relevance of chromosome position and p-value

Article of interest: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3023908/#SD1 Referring to Figure 2b of that article, if I understand correctly, the x-axis refers to the position of each variant in a ...
77 views

### Low pass sequencing has been reported to detect common variants. How low can one go and get reliable data? Is 2X pass sequencing analysis possible?

I would like to use low pass sequencing to replace a genotyping chip to be able to detect variants up to 0.1 % allele frequency in available population data. What is the minimum depth I can opt for to ...
• 21
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### Which GWGAS Tool is 'better', MAGMA or LDSC?

I am currently doing a project regarding gene-based analysis and gene-set analysis given a certain GWAS dataset, I only know 2 well known gene-based analysis tool which is LDSC and MAGMA. As of now, I'...
59 views

### Long-Covid (LC) GWAS project proposal: should I include a non-LC GWAS?

I am working on a project proposal for an exam, it involves a budget of 1M euros and I got to design a genomic study. I chose a GWAS to assess altered gene expression after covid19 that leads to long-...
107 views

### How to estimate the phenotypic variation explained by top SNPs from a GWAS study?

I have conducted a large-scale GWAS study and got a few significantly associated SNPs. I used GEMMA with -lmm 1 options to run ...
59 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 ...
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1 vote
513 views

### 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 ...
• 13
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### What does genotyping data and beta values for SNPs mean for GWAS study?

I have a list of Genes with their alleles (RS IDs) associated with a specific condition. I have to find their genotyping data and the beta values from published studies. I looked through several ...
31 views

### how to get access to genotypes and phenotypes used for a GWAS

I'm a master's student working on genomic prediction of complex traits using deep learning. i'm looking for a dataset of human genotypes and phenotypes that has been used for a GWAS. The only thing i ...
1 vote
433 views

### Making PLINK compatible files from VCF file without phenotype information

I have a big VCF file that I need to convert to, preferably, bed/bim/fam files that are readable by plink. Currently using plink 2. I am aware that this version of plink can be used to convert VCFs ...
• 11
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### How do I lift GWAS results to hg38?

There are some questions about lifting between reference builds, e.g. this one. But there doesn't appear to be a question about lifting a GWAS results file to a new reference build (except off-site). ...
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1 vote
47 views

### Random GWAS data generator

I was wondering if there is a tool/script/program that randomly generates GWAS data. The purpose of such a tool would be to use it for educational purposes. So you generate some random .ped, .map and ...
49 views

### 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 ...
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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, ...
1 vote
45 views

### 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
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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
131 views

### 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
82 views

### 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 ...
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1 vote
61 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
134 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 ...
1 vote
532 views

### Convert VCF to genotype table

How can I convert a VCF file into a genotype table (SNP matrix)? I have this format: ...
• 147
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### 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 ...
64 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 ...
• 841
1 vote
116 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 ...
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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
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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 ...
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1 vote
59 views

### 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 ...
87 views

### What is the state of the art for GWAS in terms of the statistical algorithm for either Case/control and Quantitative traits?

This question was also asked on Biostars I'm trying to understand what is the best algorithm for GWAS nowadays. I know we have many tools available like Plink and Hail, but currently, what is the ...