Question: Problem With Gatk Tools Not Accepting Bam File As Input
5.2 years ago by
Politz, Samuel M. • 70
Politz, Samuel M. • 70 wrote:
I am using GATK tools on the useGalaxy main server to detect variants in a mutant C. elegans whole genome sequence obtained with an Illumina instrument (my own data). The first GATK tool I tried to use, Realigner Target Creator, gave me an error message. In the tool window, my input file (a BAM file previously run through Add or Replace Groups) did not generate an error, but the reference genome file (ce10) which I specified as found in History, produced the following reference list-specific error: "History does not include a dataset of the required format/build". I got the same error when I tried to use this input file to run the GATK Depth of Coverage tool. I have searched Galaxy mail archives for this error, and have found other examples, but none involving these tools. The ce10 database was listed in the History attributes of the BAM file I used, and this database has worked with all of the Galaxy tools I used up to this point. Something about the ce10 format is unacceptable to GATK, or it is not even picking it up from the History. I don't know how to access ce10 to check its format. I have only found the inbuilt reference genome files in Galaxy in drop-down menus for each tool. Searching the GATK site for solutions has not been helpful, because they suggest GATK-specific functions to fix the format such as Create Sequence Dictionary. I don't have access to these tools within the Galaxy main server. Can someone suggest a workaround or a direct solution?
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