GWAS in python?

Question

[Athena]

Is GWAS in python instead of R? I tried looking for one and some parts of the analysis is written in R and some are written in python. The one I looked at was this https://github.com/frankvogt/vcf2gwas which I am not sure if this included QC portion

[Ram]

Hi,

Is this also you? https://bioinformatics.stackexchange.com/questions/21713/gwas-in-python

Answer 1

[Axzd]

Technically speaking, nothing done in R can't be replicated in Python. I don't know what you are trying to do. Still, if you know Python and do not know R, you should be able to do everything in Python, UNLESS there is a very specific task and the library to do it only exists in R (you could still re-write it in Python, but ok, that would require time and a good knowledge of Python). There are ways to call R from inside Python calling R from Python, or you could use a separate script. That said, your link doesn't seem to use R at all. I strongly feel it's just down to personal preferences and training. For example, I was trained to use R for plots. But Python is perfectly able to produce good plots. I think you get the idea.