CODEWITHSUNDEEP
bioinformaticsvcf-variant-call-formatvcftoolspicard
user2966591
user2966591

Reputation: 93

VCF4.2 file not recognised by GATK

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?

Upvotes: 4

Views: 1077

Answers (0)

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