I am trying to generate Haplotype using shapeit but everytime it says shapeit command not found ..why ?

Question

[Being Bioinformatician]

I am trying to generate Haplotype using shapeit but everytime it says shapeit command not found ..why

[iraun]

Have you added the executable file shapeit to your /bin/ directory?

Answer 1

[WouterDeCoster]

Based on what you write, shapeit is not in $PATH (the location in which your shell will look for executables) Where did you install it? An easy solution is to put a shortlink in your bin folder, e.g.: (or to any other folder listed in $PATH, check with

ln -s /path/to/where/you/extracted/shapeit ~/bin/

or to any other folder listed in $PATH, check with:

echo $PATH

[Being Bioinformatician]

Its working now Thank you .