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Questions tagged [gwas]

Genome-wide association study

Wikipedia

In genomics, a genome-wide association study (GWA study, or GWAS), also known as whole genome association study (WGA study, or WGAS), is an observational study of a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait. GWA studies typically focus on associations between single-nucleotide polymorphisms (SNPs) and traits like major human diseases, but can equally be applied to any other genetic variants and any other organisms.

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Splitting very large file by value in the first column, formatting issues

I have a data file with the first column "Site", which contains 3 sites for the data. I need to split these data by site so that I have three files - site 1, site 2, and site 3. My thinking is that the format of the columns is problematic: Uneven…
user19194612
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loop a variable outside the file

I will try to explain it. I have a .sh file that do a gwas for each cromosome in bash. This .sh file works but I would like to do a loop to automatize it instead of changing the cromosome (from 1 to 22) each time I do it. I will put a part of a code…
bubu kerokero
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model not converged when fitting SAIGE null model

When I fitted the null model in SAIGE step2 of single-variant test, it showed like following: seqFitNullGLMM_SPA(pheno~age+sex, phenotye, grm, trait.type="quantitative", sample.col="IID", maf=0.005, missing.rate=0.01) Filtering…
Wenbo Zhang
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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: (Map SNP IDs to genome coordinates) Is this possible in R - and if so, how?
user169605
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GWAS SOMMER r2 value and marker size effect in sommer 4.2.0

I am trying to get the r2 values and size effect for each marker in a GWAS using the GWAS function in the r package "sommer". From the documentation I see they should be in the object mix1$scores: scores A dataframe with as many columns as markers…
Michel Colombo
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R - How to run a GWAS analysis with no position data?

everyone! I am trying to run a GWAS analysis in R on some very simple genetic data. It only contains the SNPs and one outcome variable (as well as an ID variable for each observation). Everything I have found online includes chromosome and position…
Scott Hebert
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how to create (cases, controls, and NA) in a phenotype column based on IDs in another txt file

I am preparing a phenotype file for a GWAS. I found this conversation helpful but it is not quite what I need to do. I have a large 44k participant txt file (containing all cohort participants). Column1=FID, Column=IID, Coumn3=pseudoID I want to…
Julia
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How to Match and Extract Values between two files in python?

I have two DataFiles, and I need to match and extract the…
paul raj
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How do I load files/directories into MobaxTerm to start a Tractor (for genetics) operation?

Tractor is an operation that adds power to GWAS for an admixed individual. There are online tutorials, but I am struggling to even start running Tractor in MobaXTerm. Every time I try to run some of the code I get back "cant open file - whatever…
Dani
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How to generate random float numbers for each SNP using Python

I'm dealing with GWAS data, here I have a column name SNP_Id which is of 2 Million rows and I need to generate random float values for each SNP_Id!. How to do…
paul raj
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Custom manhattan plot multi x-axis

I have the following data set gwas_data Running head -n 23 gwas_data gives me the following table. gwas_data <- data.frame( stringsAsFactors = FALSE, udi = c("A","B","C","D","E", …
zerberus
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Pivotting the SNP Table , Converting CSV file to JSON using Bash

I'm working with GWAS data. Need help. My data looks like this: IID,rs098083,kgp794789,rs09848309,kgp8300747,..... 63,CC,AG,GA,AA,..... 54,AT,CT,TT,AG,..... 12,TT,GA,AG,AA,..... . . . As above I have a total of 512 rows and 2 Million…
user17063641
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Executing Concatenation for all rows

I'm working with GWAS data. Using p-link command I was able to get SNPslist, SNPs.map, SNPs.ped. Here are the data files and commands I have for 2 SNPs (rs6923761, rs7903146): $ cat SNPs.map 0 rs6923761 0 0 0 rs7903146 0 0 $ cat…
user17063641
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How to Extract list of all SNPs from bed file using Python

I'm dealing with GWAS data, I'm trying to Extract a list of all SNPs and their Values from the Bed file with Additive and dominance components using Python. Please help with the Python command to Extract all SNP id and their Values >>> G =…
user17063641
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Error in creating a dummy variable for plink GWAS?

I'm currently extracting phenotype/covariate data I need to run a GWAS. I am also trying to convert the 'bank_centre location' to a dummy variable. In attempting to create the data file to run the GWAS, I keep getting an error for an extra "]" in my…
Emma
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