Questions tagged [gwas]

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How to perform liftover from 38 to 37 in R?

I have some gwas summary statistics in GRCh38 that I want to lift to GRCh37. I am trying to liftover in R using this code: ...
DN1's user avatar
  • 45
3 votes
1 answer
575 views

GWAS in python?

A question similar to this has also been asked on Biostars I understand GWAS is done with R, but are any written in Python? I'm used to python and java, acclimating to R will take a bit of time and my ...
Katherine's user avatar
1 vote
0 answers
38 views

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 ...
entropy's user avatar
  • 23
1 vote
2 answers
65 views

Why does my HWE QQ plot have extreme deviation and what does it mean?

This question was also asked on Reddit I have recently completed my thesis and one of the comments was that I report on why this graph looks this way. I have tried to find a reason but the closest I ...
Shelby Labuschagne's user avatar
1 vote
1 answer
189 views

LD clump GRCh38 GWAS results

The vignette of R package ieugwasr describes a plink based wrapper function for LD clumping GWAS data using the 1000 genomes ...
Joonatan's user avatar
2 votes
1 answer
68 views

How are the "effect_allele" and "other_allele" bases chosen in a PGS file from the PGS Catalog?

How are the "effect_allele" and "other_allele" bases chosen in a PGS file from the PGS Catalog? For example, for PGS002723 (https://www.pgscatalog.org/score/PGS002723/), if I set ...
Cristian Riccio's user avatar
2 votes
1 answer
378 views

Getting nearest gene from SNP data using SNP ID, CHR, and BP

I have data from a GWAS that provides me with the SNP, Chromosome, and base-pair. My data set has thousands of SNPs. What is the easiest way to find the nearest gene for each SNP using this ...
cjsterne's user avatar
2 votes
2 answers
320 views

How to z-transform Fst and -log(p) values for genome wide selection scan?

I saw in the literature a lot genome wide scans showing $F_{ST}$ values in a 'z-transformed' format which seems to be bounded between 0 to infinity. Examples are found easily searching for 'genome-...
M. Beausoleil's user avatar
2 votes
1 answer
241 views

Genomic inflation factor distribution (lambda)

Considering that the p-value of a chi statistic(df=1) is uniform, the expected genomic inflation factor is λ=1. I show its calculation in R with the next chunk of code: ...
Gero's user avatar
  • 73
2 votes
0 answers
97 views

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 ...
Dovini Jayasinghe's user avatar
0 votes
1 answer
431 views

Identify SNP from genetic position

I am looking for a way to obtain SNP names from their coordinates (Chromosome:BP) - very much the reverse of the question answered here: (https://stackoverflow.com/questions/20251612/map-snp-ids-to-...
Gux's user avatar
  • 103
0 votes
0 answers
93 views

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 ...
user16548's user avatar
2 votes
0 answers
56 views

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: ...
Gero's user avatar
  • 73
0 votes
2 answers
350 views

Lifting snp rsid build 37 to 38

I’m looking to lift over a dataset of GWAS summary stats from build 37 to 38, including converting rsid. Downstream it is to be used for co-localisation with another dataset of build 38. Would anyone ...
medicalresearcher's user avatar
1 vote
1 answer
90 views

Allele effects by parental-origin estimated from genotyping array data

We are dealing with relatively large family data (> 1,000 trios) with genotyping array data. We would like to see the allele effects on children separately of mothers, fathers, and children, as in ...
PenguinPartyH0's user avatar
1 vote
0 answers
45 views

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 ...
7-x's user avatar
  • 21
1 vote
1 answer
311 views

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. ...
icedcoffee's user avatar
2 votes
0 answers
53 views

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 ...
Shafayet Rahat's user avatar
1 vote
2 answers
113 views

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 ...
user438383's user avatar
  • 1,679
0 votes
1 answer
73 views

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 ...
icedcoffee's user avatar
0 votes
1 answer
235 views

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 ...
John Smith's user avatar
2 votes
2 answers
84 views

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 ...
Shafayet Rahat's user avatar
4 votes
1 answer
154 views

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, ...
Vasilis Lemonidis's user avatar
0 votes
1 answer
291 views

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 ...
Shelby Labuschagne's user avatar
1 vote
0 answers
28 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 ...
Shelby Labuschagne's user avatar
1 vote
1 answer
683 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 ...
pvp's user avatar
  • 67
0 votes
1 answer
52 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 ...
Anonymous Toad's user avatar
0 votes
2 answers
160 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 ...
Kozolovska's user avatar
1 vote
0 answers
156 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 ...
7-x's user avatar
  • 21
1 vote
1 answer
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 ...
Zahrae's user avatar
  • 63
1 vote
0 answers
29 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 ...
keraC's user avatar
  • 11
1 vote
0 answers
82 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, ...
icedcoffee's user avatar
1 vote
0 answers
77 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 ...
Zahrae's user avatar
  • 63
0 votes
2 answers
86 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 ...
variancekills's user avatar
2 votes
1 answer
84 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 ...
EMPEE's user avatar
  • 21
2 votes
0 answers
58 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'...
Andreas Adinatha's user avatar
3 votes
1 answer
64 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-...
fecke9296's user avatar
3 votes
1 answer
547 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 ...
Anik Dutta's user avatar
4 votes
1 answer
138 views

How is the odds ratio of disease risk conferred by a 1-standard deviation increase in PRS calculated?

One standard deviation from the mean is commonly used to calculate a polygenic risk score for GWAS, e.g. human genetic disease. Why is this a common metric, for example why not 2-SD or 1.96 SD as in ...
Ramiro Magno's user avatar
2 votes
2 answers
2k 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 ...
J.D.'s user avatar
  • 23
0 votes
1 answer
2k 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 ...
Najeha Mohamed's user avatar
1 vote
1 answer
35 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 ...
pierre's user avatar
  • 13
1 vote
1 answer
892 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 ...
MHiller's user avatar
  • 11
1 vote
3 answers
243 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). ...
CoderGuy123's user avatar
1 vote
1 answer
74 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 ...
Cowboy_Patrick's user avatar
2 votes
1 answer
52 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 ...
Joni's user avatar
  • 133
2 votes
2 answers
68 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, ...
hpatronage's user avatar
1 vote
1 answer
64 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 ...
lalaland's user avatar
  • 113
0 votes
0 answers
204 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 ...
snowflake's user avatar
  • 147
1 vote
2 answers
247 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-...
snowflake's user avatar
  • 147