Ive seen a lot having the same problem, but I havnt found a solution yet. I have supplied 24 VCF4.1 files (http://evs.gs.washington.edu/EVS/) to GATKs CombineVariants. I get this error:
##### ERROR MESSAGE: Invalid command line: No tribble type was provided on the command line and the type of the file could not be determined dynamically. Please add an explicit type tag :NAME listing the correct type from among the supported types:
##### ERROR Name FeatureType Documentation
##### ERROR BCF2 VariantContext (this is an external codec and is not documented within GATK)
##### ERROR VCF VariantContext (this is an external codec and is not documented within GATK)
##### ERROR VCF3 VariantContext (this is an external codec and is not documented within GATK)
I have asked at GATKs support, but no good answer. I have used VCFtools for validation, they all pass, but with two, not critical warnings:
The header tag 'reference' not present. (Not required but highly recommended.)
The header tag 'contig' not present for CHROM=chr10. (Not required but highly recommended.)
Anyone knows?