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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    James Emery

    Hello Katherine Fawcett. If you want the GATK to output a GVCF you use the extra flag `--ERC GVCF` which makes the HaplotypeCaller produce a GVCF instead of a VCF. This is compatible with `--dragen-mode` but it is not part of the official tested pathway for DRAGEN-GATK so it is not as strongly guaranteed that the annotations for the non-variant sites will match with DRAGEN annotations. 

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    Katherine Fawcett

    Thanks very much, James.  Do you know if this will be made part of the official DRAGEN-GATK pipeline at some point?

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