Shape IT Phasing on Windows

Question

[salmaw]

I need help for Shape IT, can I run it on windows instead of linux as I am not familiar with Linux system

[4galaxy77]

What's your sample size and number of SNPs like? I presume (although correct me if I'm wrong) that you are planning to run it on your local PC or laptop? This could take a very long time if you have more than a few samples and SNPs and chromosomes to run. If it's possible, I would recommend trying to run it on a Linux server to speed things up. You don't need an in depth knowledge of Linux to run it, although compiling shapeit4 can be a bit of a pain sometimes.

[salmaw]

I have more than 400 samples and approx 56,1400 snps ( all autosomes). Is it possible to get intructions for setting the Shape IT on linux- though i am sure if i can get free access to the linux server? I have one more question how to convert hap files from shapeit to ped files?

Answer 1

[Kevin Blighe]

If you aiming to perform phasing via ShapeIt (and imputation via IMPUTE) and that you want to do this on a human genome sample, then it is almost certain that you will not be able to do this on Windows. These programs are not even available on Windows. At the very least, you would have to set-up a linux virtual environment on your Windows OS.

Kevin

[salmaw]

Thanks , i do realise that ShapeIt is not designed for windows, Is it possible to send me the intructons as how to set up a linux virtual enviornment on windows