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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

What is the Dragen filtering rule based on QUAL?


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    Genevieve Brandt (she/her)

    Hi jfarrell,

    DRAGEN does hard filtering on QUAL, filtering below a QUAL of 10.41. The DRAGEN-GATK method will output very similar QUAL scores to DRAGEN and will also recommend hard filtering on QUAL, though we don't have our specific filtering rule published yet.

    The first release of the DRAGEN-GATK pipeline will be focused on the best practices for single sample analysis. The filtering method on QUAL will replace VQSR for this best practices. VQSR will still be relevant for the joint calling best practices, because we will not use the new DRAGEN-GATK method for joint calling in our first release.

    Hope this helps to clarify,



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