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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

BQSR: Do read filters used by BQSR tools need to be applied to data prior to assessing the number of bases per read group?



  • Official comment
    Genevieve Brandt (she/her)

    Hi ISmolicz,

    The 100M bases per read group rule is not a hard cut off. If you have around 100M bases per read group but then lose a lot of reads in read filtering, then you might see issues. If you keep most of your reads, then BQSR should run fine. You can check the plots to see how well the recalibration worked if you are worried about your number of reads.



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    Genevieve Brandt (she/her)

    Hi ISmolicz,

    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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