cd C:/Users/Davide/downloads #set to directory with the tabix package files
tar -xf tabix-0.2.6.tar.bz2 #decompress file
export PERL5LIB=/C:/Users/Davide/vcftools/perl #set the PERL5LIB environment variable to include the vcf.pm module
cd C:/Users/Davide/vcftools #change to the target directory
make #compile the program
cd C:/Users/Davide/vcftools/bin #set directory

However when I type vcftools, I get this line

Bash: command not found"

cd c:/Users/Davide/vcftools/bin/test.t # I run a test
Can't locate Test/Most.pm in @INC (@INC contains: /cygdrive/c/Users/Davide/vcftools/perl /usr/lib/perl5/site_perl/5.14/x86_64-cygwin-threads /usr/lib/perl5/site_perl/5.14 /usr/lib/perl5/vendor_perl/5.14/x86_64-cygwin-threads /usr/lib/perl5/vendor_perl/5.14 /usr/lib/perl5/5.14/x86_64-cygwin-threads /usr/lib/perl5/5.14 .) at c:/Users/Davide/vcftools/perl/test.t line 17.
BEGIN failed--compilation aborted at c:/Users/Davide/vcftools/perl/test.t line 17.

I am using Cygwin from Windows 7A user running Ubuntu 64 bits reported the same error message so I do not think it's got anything to do with Cygwin: see Vcftools, Command Not Found !