Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Mutect2 Unable to trim uncertain bases without flow order information


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    James Emery

    Hello M Carta

    Sorry to hear about this issue. Fortunately we think this is very likely an issue that we already knew about and fixed for the GATK release related to the tool mis-identifying Minimap2 aligned data as being Ultima data because of the presence of the "tp" tag and attempting to treat it as such. We merged a fix for this code here: 
    If you try upgrading to GATK we expect that you should no longer have this issue. 

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