Questions tagged [gwas]

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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-...
3
votes
1answer
90 views

Estimating computing resources needed for a GWAS?

One of my dissertation papers is going to involve a GWAS. I have never actually run a GWAS before, and do not know how to estimate the computing resources I need for it. I asked someone on my ...
2
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0answers
19 views

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'...
2
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0answers
39 views

How is the odds ratio of disease risk conferred by a 1-standard deviation increase in PRS calculated?

I am trying to understand how the odds ratio of a 1-standard deviation increase in a polygenic risk score is calculated. I know that this is a commonly used metric of performance of a polygenic risk ...
1
vote
0answers
23 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 ...
1
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0answers
21 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, ...
1
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0answers
22 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 ...
0
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0answers
13 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 ...
0
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0answers
11 views

How to find the minimal size effect in GWAS study

I'm new to bioinformatics and I have an assigment which I have to find the minimal size effect with power=0.9 in GWAS research paper of my choosing. I don't know how I'm supposed to calculate this ...
0
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1answer
34 views

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). ...
0
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1answer
31 views

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, ...
0
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0answers
53 views

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 ...
0
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0answers
20 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 ...