Importance of population structure and LD distance in GWAS?

22 February 2023 0 3K Report

GWAS, population structure, LD distance, etc.

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Science method

Does increasing the number of individuals by copy-paste of the same indvs to perform GWAS affect the results?

I am trying to perform a genome-wide association on mitogenome variants (obtained from GATK-Mutect2) vs. phenotypes by using GAPIT. The number of individuals is seven and GAPIT function does not...

14 December 2020 8,853 3 View

How can we perform a GWAS analysis of a qualitative trait through GAPIT?

Hi,I am doing GWAS analysis on both quantitative and qualitative trait through GAPIT 3.0. Code run well for Quantitative traits but shows following error in qualitative trait Error in...

18 July 2020 9,541 5 View

Is there any minimum sample size required for GWAS?

I am investigating on SNP-trait association in a species with a narrow genetic base. I have phenotyped and genotyped 80 accessions. I would like to use GWAS for the association analysis. From...

04 July 2020 850 9 View

How can I merge two PED/MAP file sets from different chromosome builds for GWAS study in PLINK?

Hi, I have two data sets from the illumina omniexpress snp array platform. The first data set was mapped using the GRCh37 build and the second one was more recently read using the GRCh38 build....

14 June 2020 6,281 1 View

Can someone please help with inputting PLINK assoc.logistic output files into METAL to perform a meta-analysis?

I need to perform a meta-analysis of 2 GWAS studies and I need assistance with the input study files (plink --assoc.logistic) as well as the output meta-analysis file (.TBL). - Firstly, I am not...

07 June 2020 5,831 1 View

How to convert genotype file format .gen file into sample id and phenotype file format .sample file ?

Hello All, Greetings, I have 2 cohort datasets with 500 sample size each and 200 SNPS of genotype files as (example1.gen and example2.gen) as input files and trying to generate other formats...

31 May 2020 2,795 1 View

Should I test for HWE in dataset of inbred animals without random mating?

Hi, I am doing a GWAS analysis of european bison's a dog's SNPs. Right now I am doing multiple data clean up, according to previous studies and what I have learned. I was thinking, if it is ok to...

18 March 2020 3,103 3 View

What mistake in GAPIT could lead to high FDR adjusted P-values?

Can anyone suggest a reason why the association between my SNPs (90 thousand) and two quantitative traits (BMI and age) has a FDR-adjusted P-value over 0.9 for all my SNPs? I think it is very...

18 March 2020 8,080 3 View

What are the inputs for an EWAS meta-analysis in METAL?

Hello everybody, I am new with the meta-analysis in Genome Wide Data so I have this doubt. I have read METAL documentation, which is by far the most used meta-analysis software in both EWAS and...

12 February 2020 2,922 3 View

What are the inputs for an EWAS meta-analysis in METAL?

Hello everybody, I am new with the meta-analysis in Genome Wide Data so I have this doubt. I have read METAL documentation, which is by far the most used meta-analysis software in both EWAS and...

01 February 2020 1,977 2 View