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

Unable to find full Best Practices workflow for short variant joint genotyping


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    Pamela Bretscher

    Hi Kirsten Dimmler,

    This article outlines the detailed steps for running VQSR after GenotypeGVCFs in the pipeline which includes the step of making the sites-only VCFs. However, you don't need to do both hard filtering and VQSR. The article details the steps for each type of filtering which can be run on your GenotypeGVCFs output. Please let me know if this does not answer your question. 

    Kind regards,


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