My guess: you ran make. The next step is to use the installation rules in the makefile to move the newly built binaries to a system directory. For this you should run sudo mv /path/to/binaries/* /usr/local/bin/. Then make sure /usr/local/bin is in your PATH environment variable: echo $PATH. This is based on the vcf-tools documentation.

If "command vcf-subse not found" was the exact message, it's probably a typo - try vcf-subset.

I guess you have to export the vcf.pm path before using the Vcf-subset function in vcftools.

export PERL5LIB=/your-path-to-vcftools/perl

I tested all of these ways above. but it does not work and still an error says "command not found". I work with Ubuntu 64-bit on VMware workstation. in vcftools documentation it has said that :

The tools can be tested by running the script

/path/to/your/installation/perl/test.t

I ran that and got this message:

Can't locate Test/Most.pm in @INC (@INC contains: /home/ali/Documents/vcftools_0.1.9/perl /perl /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl .) at ./perl/test.t line 17.
BEGIN failed--compilation aborted at ./perl/test.t line 17.

Now I m sure you have the problems with the path. The path for exporting the vcf.pm need to be absolute. Check out the problem below.

http://www.biostars.org/post/show/51239/why-vcftools-commands-not-working/#51242