I'd like to run PLINK2 on a vcf file to do linkage pruning, followed by a PCA. The input vcf file is from a non-human …

I have a GWAS sample like this https://ftp.ncbi.nlm.nih.gov/dbgap/studies/phs001672/analyses/phs001672.pha005197.txt. I want to create a Python script that will be able to declare if the chr23 is …

I see that REGENIE GWAS software (https://rgcgithub.github.io/regenie/options/) allows the X chromosome to be included. To include the X-chromosome in REGENIE GWAS analyses, is quality control …

Hi everyone! I plan to run a GWAS using Regenie software (https://rgcgithub.github.io/regenie/). Regenie is an LMM-based GWAS software, that can handle the X-chromosome. I will …

My vcf files show chromosome variants till chromosome 14, though in upper info for contigs it mentions lengths from chr 1 to 22 and X …

I'm new to R and Limma, and I tried to analyze a data set using the Limma guide. So far, so good, but now I …

I am using mendelian randomisation (MR) approach to determine whether there is a causal effect of an exposure *X* on the outcome *Y*. To do …

Hi all, I am currently learning how to perform GWAS quality control, and I have a question on the sex check step. As I understand …

Hello friends, How to compare the genotype calls of the SNPs on chromosome X for the GWAS samples between the GWAS Plink file and the …

I'm doing a gwas with 200+samples and get the qqplot with the P-value of the logistic analysis include the PCs and age as the covariates, …