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

Realignment indels filtering 1000G

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    Genevieve Brandt (she/her)

    Hi Hanna Söderström,

    Not all resources are available for all reference versions, I don't think the file you are looking for is available. Please let me know if you still need to solve this issue and I can look into it further if you let me know which pipeline you are running.

    If you have found this file, please let us know so other GATK users in the future can know where to get it.

    Best,

    Genevieve

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    Genevieve Brandt (she/her)

    Hi Hanna,

    The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

    Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

    We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.

    For context, check out our support policy.

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