Questions tagged [gwas]

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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. ...
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2 votes
0 answers
40 views

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 ...
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1 vote
2 answers
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 ...
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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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2 answers
39 views

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 ...
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21 views

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 ...
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1 answer
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 ...
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4 votes
1 answer
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, ...
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0 votes
1 answer
64 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 ...
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1 vote
0 answers
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 ...
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1 vote
1 answer
146 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 ...
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0 votes
1 answer
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 ...
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0 votes
2 answers
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 ...
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0 votes
0 answers
25 views

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 ...
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1 vote
0 answers
72 views

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 ...
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1 vote
1 answer
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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 ...
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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 ...
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1 vote
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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, ...
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0 votes
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19 views

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 ...
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1 vote
0 answers
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 ...
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2 answers
65 views

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 ...
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2 votes
1 answer
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 ...
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2 votes
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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'...
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3 votes
1 answer
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-...
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3 votes
1 answer
104 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 ...
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4 votes
0 answers
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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2 answers
506 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 ...
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1 answer
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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 ...
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0 votes
1 answer
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 ...
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1 vote
1 answer
432 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 ...
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1 answer
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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
1 answer
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 ...
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2 votes
1 answer
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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0 votes
1 answer
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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, ...
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1 vote
1 answer
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 ...
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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 ...
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1 vote
2 answers
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-...
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  • 147
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1 answer
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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 ...
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1 vote
1 answer
60 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 ~...
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  • 147
1 vote
1 answer
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 ...
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1 vote
1 answer
531 views

Convert VCF to genotype table

How can I convert a VCF file into a genotype table (SNP matrix)? I have this format: ...
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0 answers
22 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 ...
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0 votes
2 answers
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 ...
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  • 841
1 vote
2 answers
115 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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  • 107
0 votes
1 answer
73 views

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 ...
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3 votes
1 answer
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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
1 answer
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 ...
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3 votes
1 answer
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 ...
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0 votes
2 answers
87 views

CRISPR screening and systems biology

I am not sure how to tackle this one, so I’ll explain the general idea I have in mind. Given results of a CRISPR knockout screening experiment (like in this paper) with two types of assays: control ...
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  • 1,347
0 votes
1 answer
150 views

Simulating phenotype with the 1000 Genomes Project

I'm looking for a way to simulate phenotypes against a real SNP data source, such as the 1000 Genomes. It must be free for commercial purpose (Eg.: MIT license). Any recommendation? I'm trying to use ...
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