[Vcftools-help] error: "Use of uninitialized value in hash element"

SourceForge Headquarters 1320 Columbia Street Suite 310 San Diego, CA 92101 +1 (858) 422-6466

I am trying to merge two vcf containing multiple samples but the process 
gives continuosly this error
Use of uninitialized value in hash element at 
/share/apps/genomics/vcftools-0.1.4a/perl/Vcf.pm line 498, <$__ANONIO__> 
line 6.
Use of uninitialized value in hash element at 
/share/apps/genomics/vcftools-0.1.4a/perl/Vcf.pm line 498, <$__ANONIO__> 
line 6.
and the resulting file appears like that
1    13438    .    CTT    C    167.00    PASS    
AC=1;AN=344;DP=110;HP=4;NF=3;NFS=23;NR=7;NRS=37;SF=1    GT:GQ    .    
.    .    .    .Use of uninitialized value in hash element at 
/share/apps/genomics/vcftools-0.1.4a/perl/Vcf.pm line
  498, <$__ANONIO__> line 6.
Use of uninitialized value in hash element at 
/share/apps/genomics/vcftools-0.1.4a/perl/Vcf.pm line 498, <$__ANONIO__> 
line 6.
Use of uninitialized value in hash element at 
/share/apps/genomics/vcftools-0.1.4a/perl/Vcf.pm line 498, <$__ANONIO__> 
line 6.

1    1115555    .    C    CT    40.00    PASS    
AC=1;AN=344;DP=12;HP=1;NF=1;NFS=3;NR=1;NRS=2;SF=1    GT:GQ    .    .    
.    .    0/0:0    0/0:0    0/0:0    0/0:0    0/0:0    0/0:0    0/0:0    
0/0:0    0/0:0    0/0:0    0/0:0    0/0:0    0/0:0    0/0:0    0/0:0    
0/0:0    0/0:0    0/0:0    0/0:
0    0/0:0    0/0:0    0/0:0    0/0:0    0/0:0    0/0:0    0/0:0    
0/0:0    0/0:0    0/0:0    0/0:0    0/1:40    0/0:0    0/0:0    0/0:0    
0/0:0    0/0:0    0/0:
0    0/0:0    0/0:0    0/0:0    0/0:0    0/0:0    0/0:0    0/0:0    
0/0:0    0/0:0    0/0Use of uninitialized value in hash element at 
/share/apps/genomic
s/vcftools-0.1.4a/perl/Vcf.pm line 498, <$__ANONIO__> line 50.
Use of uninitialized value in hash element at 
/share/apps/genomics/vcftools-0.1.4a/perl/Vcf.pm line 498, <$__ANONIO__> 
line 50.

I also had to clean the file from messages like
"Using colum name 'UCL.._data" which should be a STDERR but appear to be 
directed into the file

I tried the same using just one sample, using vcf-concat on the snps and 
the indel files, but it doesn't accept it since it says the colums have 
different names (one has been converted from 3.3 samtools to 4.0 with 
the vcf-convert tool, the other has been produced by dindel.

thanks for your help,
Francesco
-- 