VCFtools 0.1.9 perl Vcf.pm does not work with perl 5.14 or newer. use the VCFtools svn or this patch.

Error: bare qw() in a for loop: for $x qw() {} # deprecated. It needs to be surrounded by parents. . See my previous blog entry about this feature.
 patch:

$  diff Vcf.pm Vcf.pm-ori 
1622c1622
<         for my $key (qw(fmtA fmtG infoA infoG)) { if ( !exists($$out{$key}) ) { $$out{$key}=[] } }
---
>         for my $key qw(fmtA fmtG infoA infoG) { if ( !exists($$out{$key}) ) { $$out{$key}=[] } }

Now all tests work OK. [upate] the svn version 779 of Vcf.pm is fixed

for my $key (qw(fmtA fmtG infoA infoG)) { if ( !exists($$out{$key}) ) { $$out{$key}=[] } }