[galaxy-user] error in .vcf .bcf files from freeBayes and mPileup

Hi, I run a very regular BWA mapping with a public reference genome sequence and then I tried to do some variant analysis with both mpileup and freeBayes tools. These jobs run just fine, but then when I went to convert these files to a .maf format or using the bcf2vcf converter there were errors in the metadata and the jobs couldn't run. One main error in the freeBayes output gave the exception: "components must have same text length". I also tried to run some vcf to maf converter from command line (python tool) on the downloaded file and also didn't work. Any suggestion on what's wrong with the file? thanks stefano