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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

PathSeq output

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    Genevieve Brandt (she/her)

    Hi Arman Ardalan,

    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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    Arman Ardalan

    Hi Genevieve,

    Thank you for your note. However, my impression was that PathSeq is already a tool under GATK, and that the issues I asked about were exact cases of "abnormal results from the tools". I was therefore not able to relate much to your response.

    It was required by the PathSeq developers whom I had contacted first that I post my questions here, so more users can benefit from possible discussions.

    /Arman

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    Genevieve Brandt (she/her)

    Hi Arman Ardalan, we need to get more information to be able to get insight in this case. To get better results with this pipeline you will need to experiment with different parameters using your specific data. The defaults won't work for every case. We recommend that you specifically look at the filtering phase of the pipeline because that may be why you are not getting the final results that you expected.

    For further support, please post a detailed explanation of what you have tried and if anything in your data could explain some of these issues. Please also include specific cases of taxa that were not included and evidence that they should be included in the final output.

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