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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

Map reads to a reference with alternate contigs like GRCH38 using GATK4

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    Genevieve Brandt (she/her)

    Hi neethukrishna Kausthubham, we are still in the process of updating that article. You should be able to test out the main steps, then adapt the pipeline with GATK4 tools instead of GATK3 tools. Many of the tools have the same name, so it may be easy to adapt. 

    You can also see this article for the Germline short variant discovery (SNPs + Indels) Best Practices, as well as Data pre-processing for variant discovery Best Practices. These are up to date with GATK4 so they have the correct command usage. 

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    neethukrishna Kausthubham

    Genevieve Brandt (she/her), thank you for the reply. I was just going through the alt-aware alignment and I am not very clear how to deal with the downstream analysis. But gradually I may be able to figure this out.

    It would be great if anyone can address the following concern.

    1) In a clinical context, if we use the reference which contains only the primary assembly of GRCH38  then will it make a huge impact on the downstream analysis?
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    Genevieve Brandt (she/her)

    Hi neethukrishna Kausthubham,

    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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