I am currently working on a mendelian randomization study, and I have downloaded the datasets needed from the ieu opengwas project (mrcieu.ac.uk) in .vcf format. I do not have access to an R statistical package.
Many thanks,
Radwan
Everyone has access to R! Just download it and get going.
https://www.r-project.org/
TIp: Download RStudio, which is a brilliant interface for R.
https://posit.co/products/open-source/rstudio/
As Ronán said, you do have access.
But you may also have a look at the file specification:
https://samtools.github.io/hts-specs/VCFv4.2.pdf
It's a simple text file, so you can open such files with any text editor. You can also import the file in Excel (and convert text in columns).
If not, you can work the r online on a posit server, it has some free options.
https://login.posit.cloud/
here you will find a VCF to XLS converter, it can be useful
https://products.groupdocs.app/en/conversion/vcf-to-xls#:~:text=C%C3%B3mo%20convertir%20VCF%20a%20XLS&text=Haga%20clic%20dentro%20del%20%C3%A1rea,al%20formato%20de%20resultado%20XLS.
If you are working on a Mendelian randomization study, there is probably no need to directly download the .vcf files and open them locally.
As said before, R is freely available and all of the packages are easy to download and use.
Try using the "TwoSampleMR" package specifically designed for Mendelian randomization analyses. Using this package you can access the repository of GWAS summary association data (the IEU GWAS database), easily extract the exposure and outcome data and perform the MR analysis.
Many thanks everyone, I downloaded R and Rstudio, and worked away using the TwoSampleMR package. It’s taken a while to get used to, but I think I’ve got it now.