Questions tagged [gwas]
The gwas tag has no usage guidance.
15
questions with no upvoted or accepted answers
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answer
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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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101
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Input for --score in PLINK 1.9 when generationg PRS using GWAS summary statistics
I'm conducting a simulation and I need to obtain polygenic risk scores (PRS) using genome wide association studies (GWAS) summary statistics.
It is known that the GWAS will give BETA and OR for ...
2
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0
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56
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LD block labels annotation for GWAS summary data
I have a txt file summarising the result of a GWAS on an European population. Its structure is the next one:
...
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2
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54
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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 ...
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60
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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'...
1
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0
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42
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PLINK linear association testing command with an interaction and 2 covariates term
I am trying to write the right command for my association testing using PLINK 1.9 but I could not find a clear answer so far and not sure how to wrtie it correct.
I have genotype variants called and ...
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1
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47
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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 ...
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28
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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
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0
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156
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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 ...
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1
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29
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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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1
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83
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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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79
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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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1
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33
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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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96
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Help sought with GWAS and vcf files, lack phenotype labels
This question has also been asked on Biostars
Hi, I am very new to this area, and I am taking a class about bioinformatics. For an independent project assignment, I need to do a GWAS. I am using the ...
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211
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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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