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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

GATK4 ModelSegment Error Allelic-count sites must be identical across all samples

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    Anthony Dias-Ciarla

    Hi Linghao Song,

    Thank you for writing to the GATK forum! We hope we can help you sort this out.

    Please try running ModelSegments again with the --minimum-total-allele-count-case parameter set as the current default value of 0.

    I hope this helps; please let me know if that works!

    Best,
    Anthony

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    Linghao Song

    Thank you Anthony!

    I think reducing -minimum-total-allele-count-case resolves our issue! 

    Best,

    Linghao

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