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

Too many variants after WGS workflow for a pig line


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    Genevieve Brandt (she/her)

    Hi Alia Parveen,

    After joint calling your variants, your final VCF needs to be filtered. GATK calls many possible variants and without filtering you can get many false positives.

    Hopefully this tutorial will help you out: (How to) Filter variants either with VQSR or by hard-filtering

    You can also check out this troubleshooting document for looking into HaplotypeCaller variant calls.

    However, a lot of our recommendations are based on human data, so researchers with non-human data might be able to help you out more. I'm going to move your post into the Community Discussions section of our forum to the topic Special GATK use cases. You can read more about our forum guidelines here.

    Hope this helps, and hopefully other researchers can help out as well.



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