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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

HaplotypeCaller calling whole chromosome as NON_REF



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    Anthony DiCi

    Thank you for your post, Tommy Phannareth ! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions. 

    Please see our Support Policy for more details about how we prioritize responding to questions.

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    Genevieve Brandt (she/her)

    Hi Tommy Phannareth,

    Thanks for writing into the GATK forum and for your patience about this issue you are seeing. I am wondering if a majority of your reads are getting filtered out? How many reads do you have in your input bam?

    Here's where I see that information:

    11:18:24.703 INFO  HaplotypeCaller - 151718 read(s) filtered by: MappingQualityReadFilter
    0 read(s) filtered by: MappingQualityAvailableReadFilter
    0 read(s) filtered by: MappedReadFilter
    0 read(s) filtered by: NotSecondaryAlignmentReadFilter
    0 read(s) filtered by: NotDuplicateReadFilter
    0 read(s) filtered by: PassesVendorQualityCheckReadFilter
    0 read(s) filtered by: NonZeroReferenceLengthAlignmentReadFilter
    94657 read(s) filtered by: GoodCigarReadFilter
    0 read(s) filtered by: WellformedReadFilter
    246375 total reads filtered

    Let me know if this is the case. If not, we can continue to look into possible issues. Another helpful piece to see is if you look at the input bam in IGV and if you pick out some test sites where you would expect to see variance. Then, we can track what is going on at those sites.

    Let me know,


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    Genevieve Brandt (she/her)

    Hi Tommy,

    We haven't heard back from you so we're going to close out this ticket in our system. If you still require assistance, simply respond to this thread and we'll be happy to pick up where we left off!

    Kind regards,


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