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Override index type/location on per file basis

TechnicalVaultTechnicalVault Cambridge, UKMember Posts: 111 ✭✭✭

I'm getting an error "An index is required, but none found" for files from the GATK resource bundle. In this case hapmap_3.3.b37.vcf.gz from your bundle has hapmap_3.3.b37.vcf.idx.gz in the same directory. I suspect this is because my input VCF file is tabix indexed something in GATK has decided that everything else must be. Is there any way to override this? I'm guessing it might be something to do with tribbles? But I can't seem to find the relevant bit of documentation that explains this.

Martin Pollard, Human Genetics Informatics - Wellcome Trust Sanger Institute and Genetic Epidemiology Group - WTSI & Cambridge University


  • TechnicalVaultTechnicalVault Cambridge, UKMember Posts: 111 ✭✭✭

    Scratch that I'm being thick, I'd assumed the indexes in the resource bundle were for the compressed files as we do with Tabix files. Turns out they're for the uncompressed files. Apologies

    Martin Pollard, Human Genetics Informatics - Wellcome Trust Sanger Institute and Genetic Epidemiology Group - WTSI & Cambridge University

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