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  • Create vcf tribble index?

    Hi, I'm using the GaTK to call variants, and afterward I somehow managed to delete some of the .vcf.idx index files. Without those files the GaTK can't read the vcf files. Is there a way to (re-) build the .idx indexes without re-running the UnifiedGenotyper? Couldn't find one in the GaTK documentation. (I read about tabix, but he requires bgzipped input, which I'm not sure the GaTK can handle)
    Thanks!

  • #2
    You can generate the index using igvtools, either from the command line or from the IGV gui.

    Actually, the command line version never works for me. It gives the error, "Exception in thread "main" org.broad.tribble.TribbleException$InvalidHeader: Your input file has a malformed header: We never saw a header line specifying VCF version". But running the tool from inside IGV has no problem.

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    • #3
      I run the tool from inside IVG and it gives the error: "Your input file has a malformed header:The FORMAT field was provided but there is on genotype/sample data"

      Do you know how to fix this?

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