I had similar problem with vcftotab on Galaxy Main (Missing information VCFtoTab-delimited) and tried to workaround this problem using vcftotab on Galaxy EU and was asked to issue this similar problem.
Using vcftotab on my data leaves me with lots of missing information from the INFO field. Even when using bcftools norm (accordingly to the advice in the Galaxy Tutorial “somatic variant calling”), cleaning out all the information on the Info field with SnpSift rmInfo and annotating it with SnpEff again (which is the annotation tool used in the just mentioned tutorial) I keep having lots of missing information.
I tried other tools in order to query my annotated variants, such as bcftools query. However, I encounter the problem, that for information in the Info field with the same INFO Tag (gnomad_exome and gnomad_genome for Non-finish are both annotated to my variants using annovar with AF_nfe) only one value is represented in the query output.
Eventually I could manage to install a Galaxy docker and vcftotab worked perfectly on the docker. However, snpeff does not work properly on my docker (SnpEff Error java.lang.OutOfMemoryError: Java heap space). So right know I cannot apply my workflow on Galaxy Eu or my own instance, because either way one of the tools used (snpeff or vcf2tsv) is not working.
I am glad for any help!
All the best Rose.