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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

How to call SNPs from mapped reads with mapping quality MAPQ zero

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    Bhanu Gandham

    Hi ,

    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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    danilovkiri

    Hi Kaitao Lai

    The documentation page for GATK HC contains the solution. Specifically, HC applies MappingQualityAvailableReadFilter and MappingQualityReadFilter, which imply the functionality you are looking for.

    Please refer to https://gatk.broadinstitute.org/hc/en-us/articles/360037225632-HaplotypeCaller#--disable-read-filter --disable-read-filter option for disabling these filters. It might help, though disabling read filters is dangerous in terms of HC stability. You can also use --disable-tool-default-read-filters if necessary. All the default read filters are listed and highlighted at the top of the documentation page.

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    Giulia Biancon

    Hi! I have the same problem with GATK4 Mutect2. I need to disable mapping quality filters for multi-mapping reads but if I disable all the filters one by one with --disable-read-filter I get an error and Mutect2 doesn't work. I also used --disable-tool-default-read-filters true but I got the same error. Is there a way to solve this issue with GATK4? 

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    Genevieve Brandt

    Hi Giulia Biancon, please submit a new post, since you are asking about Mutect2 and the above question is regarding HaplotypeCaller. We will need to know your GATK version, the exact GATK command used, and the entire error. Please note that we do not recommend disabling read filters, so depending on your error, we may not be able to provide support. Here is the Mutect2 documentation for your reference.

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