Episode #125 of the Stack Overflow podcast is here. We talk Tilde Club and mechanical keyboards. Listen now

Questions tagged [gwas]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
0
votes
1answer
26 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
vote
1answer
53 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 ...
2
votes
2answers
161 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
votes
1answer
35 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 ...
1
vote
1answer
89 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 ...
0
votes
0answers
16 views

Number of recombination events from GWAS data per person

Is there a way to calculate number of recombination events from GWAS data per person? Autosomal chromosomes. I looked online to see if any tool/package is available but none. I could phase data ...
1
vote
1answer
165 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
votes
1answer
53 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 ...
4
votes
0answers
39 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 ...
0
votes
1answer
88 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 ...
2
votes
0answers
63 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 ...
3
votes
0answers
59 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
votes
2answers
871 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
votes
1answer
47 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 ...
1
vote
2answers
2k 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?
5
votes
2answers
506 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 ...
4
votes
1answer
485 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 ...
5
votes
1answer
584 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: ...
4
votes
3answers
525 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
votes
1answer
321 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. (...
5
votes
3answers
160 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
votes
1answer
155 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, ...