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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

GenotypeGVCFs produces bizarre mapping quality distribution


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    Pamela Bretscher

    Hi Daniel Nondorf,

    Thank you for writing in. This may be an expected result just depending on your input data and what tools you have run. Can you take a look at the default read filters listed in the HaplotypeCaller documentation that are automatically applied to see if this helps explain your results? (or similar documentation for tools you ran prior to GenotypeGVCFs) If this is not helpful, could you provide more information about your data and the tools you have run so far? 

    Kind regards,


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