Question: Shape IT Phasing on Windows
0
gravatar for salmaw
13 days ago by
salmaw0
salmaw0 wrote:

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

forum genome • 83 views
ADD COMMENTlink modified 13 days ago by Kevin Blighe69k • written 13 days ago by salmaw0

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.

ADD REPLYlink written 13 days ago by 4galaxy77100

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?

ADD REPLYlink written 13 days ago by salmaw0
1
gravatar for Kevin Blighe
13 days ago by
Kevin Blighe69k
Republic of Ireland
Kevin Blighe69k wrote:

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

ADD COMMENTlink modified 13 days ago • written 13 days ago by Kevin Blighe69k

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

ADD REPLYlink written 13 days ago by salmaw0
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