Questions tagged [gwas]

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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 ...
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2answers
22 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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2answers
55 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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1answer
30 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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1answer
16 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 ...
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1answer
47 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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1answer
62 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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76 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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1answer
67 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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1answer
32 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).
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1answer
91 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 ...
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2answers
645 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 ...
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1answer
61 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 ...
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1answer
210 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 ...
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1answer
561 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 ...
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1answer
89 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 ...
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0answers
62 views

making my own population allele frequency table for input to IADMIX from Gnomad data (population admixture)?

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 ...
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1answer
116 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 ...
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0answers
104 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. Or, perhaps ...
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0answers
71 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 ...
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2answers
1k 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 ...
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1answer
56 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 ...
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2answers
4k 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?
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2answers
724 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 ...
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1answer
710 views

Adjusting phenotypes by regressing out covariates

I'm trying to use the bfGWAS tool, which analyses GWAS data and integrates functional annotations to identify casual SNPs (paper and github). In the user manual, it states: We recommend first ...
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1answer
773 views

How to deal with correlated SNPs in GWAS?

I have population SNP data in VCF format, and I found that some SNPs have a great similarity across samples(> 99%). For example: ...
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3answers
820 views

Is there any difference between SNPs 'AG' and 'GA' in association analyses?

I am using plink to check the association between a phenotype and the SNPs of a gene. plink says the phenotype is significantly associated with a SNP on that gene, and when I check the SNP alleles, ...
6
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1answer
381 views

Where can I find a GWAS data set about genotypes and phenotypes for Zebrafish and rice?

My goal is to work on GWAS method development as a research project. However, human genome data are usually confidential because of the identification problem, so it's very hard to get them. (...
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3answers
175 views

Where can I find a database that has phenotype information together with associated SNPs?

I have been searching for a long time and the furthest I got is some database with the functional description for genes. Then, I have to parse these descriptions manually to figure out the association....
6
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1answer
168 views

Filtering imputed GWAS SNPs based on a MAF difference of 10%

There are many posts on the web regarding QC steps pre and post-imputation. Does applying below (new?) 10% MAF difference rule make sense, pitfalls? Here is the process: Get MAF for imputed set, ...