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

Haplotypecaller usage (version decrepancy)



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    Bhanu Gandham

    Hi stella


    Since we do not support GATKv3 anymore I am not going to be able to provide a recommendation on results from GATKv3 tools. We recommend upgrading to GATKv4.

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    Dear Bhanu Gandham, 
    Thanks for your reply.
    Sincerely yours,
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