vcf-compare: tabix index is broken

[tomkina]

Hello,

I'm trying to compare two vcf-files (see the attachment) using vcftools_0.1.12b. The files have one mismatched varinat (chr9). This variant is not found by vcf-compare tool since the tabix index is broken. What is the problem with my vcf file? Both vcf files were created with Ion PGM instruments.

Thanks,
Tamara