Questions tagged [gwas]

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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 ...
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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, ...
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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 ...
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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 ...
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2answers
60 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 ...
2
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1answer
61 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 ...
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'...
3
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0answers
36 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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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 ...
3
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1answer
46 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 ...
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 ...
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2answers
126 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 ...
0
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1answer
81 views

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 ...
0
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1answer
26 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 ...
0
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1answer
178 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 ...
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). ...
1
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1answer
39 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 ...
2
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1answer
48 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 ...
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, ...
1
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1answer
44 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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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 ...
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2answers
103 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-...
0
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1answer
55 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 ...
1
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1answer
45 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 ~...
1
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1answer
104 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
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1answer
237 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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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 ...
0
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2answers
43 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 ...
1
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2answers
101 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 ...
0
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1answer
56 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 ...
2
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1answer
87 views

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 ...
1
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1answer
57 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 ...
3
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1answer
78 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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2answers
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 ...
0
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1answer
130 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 ...
0
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1answer
44 views

significant SNPs to annotated candidate genes

I have performed GWAS and got some significant SNPs. How can I get candidates genes in the flanking regions of those SNPs and also their functional annotations (eg. KEGG).
1
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1answer
104 views

Pandas automatically rounds GWAS P-value

I am working with a specific GWAS. If I were to run this on the command line grep <rs_id_of_interest> GWAS.txt I would see the GWAS p-value to be on the ...
4
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2answers
1k views

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 ...
2
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1answer
120 views

PLINK - Transposed BED file?

I'm currently working with the PLINK file system to store large amounts of genotype data. The plain format consists of three files, two files for storing phenotype and marker information as well as ...
2
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1answer
390 views

how do I convert a vcf file for a GWAS study (using R package vcfR)

I have a vcf file with individual level genetic data, that I read using the R package vcfR ...
3
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1answer
1k views

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 ...
2
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1answer
154 views

Parallel in PLINK for linear association for SNP effects

I am doing linear association calculations for SNP effects, I see it take a lot of time to do, does anyone have any experience in parallelizing this job. I have used ...
6
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0answers
85 views

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 ...
1
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1answer
153 views

Odds ratio calculations in GWAS paper

Posting here because the reddit thread I made didn't gain any traction. I'm having a little bit of trouble understanding how the odds ratio was calculated in this table, specifically the OR marked ...
3
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3answers
282 views

Is there a way to do GWAS on phenotype data that is not normally distributed?

Is there a way to do GWAS on phenotype data that is not normally distributed? For example, if you were measuring a trait as a proportion, and the majority of the data consisted of 0.00 with a 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 ...
3
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2answers
2k views

How to filter info score post-imputation?

this is a very basic question, but I cannot find it explicitly stated anywhere: When exactly should I filter the info scores after imputation? I did imputation in Impute2 and am planning on using ...
3
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1answer
61 views

Assuming that we have the following SNP and phenotype data, is the SNP significantly associated with the phenotype?

So if I attempt this question using their method I put the data of genotype and phenotype into a data frame in R then use lm() to do linear regression and ...
2
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2answers
7k views

What are the differences between GWAS and QTL mapping? [closed]

What are the differences between the two methods? What advantages does one have over the other, and what are their limitations relative to one another?
6
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2answers
1k views

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 ...