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A question similar to this has also been asked on Biostars

I understand GWAS is done with R, but are any written in Python? I'm used to python and java, acclimating to R will take a bit of time and my advisor wants some data analyzed. I plan on using R but given the deadline, I want to finish the analysis in Python.

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    $\begingroup$ Please edit your question and give us (a lot, a huge lot) more context. Tell us what input data you have, what kind of analysis you want to do (do you have the results of the GWAS study or are you trying to run the study itself?), what species and anything else that could be relevant. Of course you can do it in python, you can do anything in any programming language, so you really need to narrow this down to something very specific that can be answered in a few lines. $\endgroup$
    – terdon
    Oct 16, 2023 at 15:47
  • $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Oct 16, 2023 at 21:33
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    $\begingroup$ I would adapt PLINK. Whilst Biopython pop gen could be used it is better to use a standalone package. $\endgroup$
    – M__
    Oct 17, 2023 at 16:06
  • $\begingroup$ You can use Python to wrap around command line tools $\endgroup$
    – BigMistake
    Oct 17, 2023 at 21:01

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It doesn't (really) matter what language a piece of GWAS software is written in. SAIGE is written in a mix of R and C++. BOLT is written in C++. You shouldn't be writing a GWAS analysis from scratch, as it ends up being a very complex piece of software. You will almost certainly be interacting with the command line, when running a GWAS, so my advice is to find the software which is most suitable for your piece of analysis, not one which is written in a programming language you like.

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