Questions tagged [gwas]
The gwas tag has no usage guidance.
84
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Applying colocalization analysis in Asian populations
I am planning to add colocalization method as a post-GWAS analysis in my study which is solely based on east Asian populations. I have noticed that coloc, enloc and eCaviar are being commonly used for ...
- 21
1
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384
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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. ...
- 155
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55
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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 ...
- 315
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2
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133
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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 ...
- 1,719
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91
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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 ...
- 155
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votes
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264
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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 ...
- 109
3
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2
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99
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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 ...
- 315
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158
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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, ...
0
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1
answer
326
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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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0
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29
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
...
1
vote
1
answer
798
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 ...
- 67
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59
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 ...
0
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2
answers
191
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 ...
- 251
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160
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 ...
- 21
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37
views
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 ...
- 63