Genome Analysis Toolkit

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

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    Pamela Bretscher

    Hi Bekah W,

    When the mapping qualities are very good at a particular site, it is expected for the MQ value to be around 60. This article explains a little bit more about what is expected for the MQ value. It seems that this is likely an indication that your reads are very high quality, but if you are still concerned or unsure, could you provide some more information about what you are seeing?

    Kind regards,


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