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 Maarten Nijenhuis. We have a number of resources available for coming up to speed on using our tools for VariantCalling. You can find some old recordings of our GATK workshop material that goes over our best practices here We also have a set of FAQ tutorials here:

    Those links mostly goes over the basics for how our calling pipeline works rather than your specific use case organism. There are two aspects of what you describe that I suspect will cause problems, the first of which is that you are using amplicon sequencing which can cause lots of problems in our tools. You can search the forums for advice on this sort of calling but our general advice is to drop MarkDuplicates from your pipeline and run HaplotypeCaller with the extra argument:

    --dont-use-soft-clipped-bases true

    Furthermore you should also be able to address the ployidy by adjusting the ployidy setting in HaplotypeCaller with this argument:

    --ploidy 4
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    Maarten Nijenhuis

    Thank you James Emery. I will start by studying these links.


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