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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?

toolic
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user2966591
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  • I finally figured it out: It was something off the the VariantAnnotator vcf from GATK, I re-ran it and used the new file, I also deleted the old index file. The manual correction of the ESP VCF works! Its a bit boring, but it does the job. Hope this help anyone else getting this error! Replace all chromosome names manually using "find & replace" in Textedit. Its something about the formatting thats off. – user2966591 Nov 12 '13 at 16:56
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    If you solved the problem you should put the solution in an answer. – ThisSuitIsBlackNot Nov 12 '13 at 17:19

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