vcf-merge error

[emanuelak]

Hello everyone,

my goal is to merge several vcf files (one per individual) into a single file for further analysis.
Using vcf-merge I get the following error and the output is interrupted :

Uh: 0 vs 0
$VAR1 = [];
$VAR2 = [];

at /home/vcftools_0.1.11/perl//Vcf.pm line 177
Vcf::throw('Vcf4_1=HASH(0x26e6548)', 'Uh: 0 vs 0\x{a}', '$VAR1 =
[];\x{a}', '$VAR2 = [];\x{a}') called at /home/vcftools_0.1.11/perl//Vcf.pm
line 1956
VcfReader::format_haplotype('Vcf4_1=HASH(0x26e6548)', 'ARRAY(0x2767b00)',
'ARRAY(0x2735fe8)') called at /home/vcftools_0.1.11/perl/vcf-merge line 486
main::merge_vcf_files('HASH(0x26712e0)') called at
/home/vcftools_0.1.11/perl/vcf-merge line 12

Can somebody please help me understand what is the problem?
When I run vcf-validator on my files, I get that there are more values than the expected (1) in 2 tags of the INFO field.

I tried to use GATK CombineVariants tool and I get the error
VCFHeaderLine: key cannot contain angle brackets
even if I remove all the unnecessary lines from the header.

Any suggestions would be very helpful.
Thank you

Emanuela