shapeit command not found - shapeit installation for GWAS phasing

Question

I would like to install the shapeit for GWAS phasing and impuation. I downloaded the Shapeit version for macos from Shapeit website:

https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#download

I extracted the file and got the shapeit execuable file, example folder, and licience file.

Next, I open the terminal in Mac, cd the directory to shapeit folder and type the command line as the website guided:

shapeit -B gwas \
        -M genetic_map.txt \
        -O gwas.phased

And I got the response:

shapeit command not found.

I guess that means i need to install the shapeit or set a path for shapeit. But I don't know how to do. I am very new with Macos.

Could someone help me ?

Answer 1

1. Try ./shapeit instead of shapeit , or
2. Run cp shapeit /usr/local/bin first and try again.