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

identify heteroplasmic variants MTLowHeteroplasmyFilterTool



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    Bhanu Gandham

    Hi ,

    I am going to move your post into our Community Discussions -> General Discussion topic, as the Special GATK Use Cases topic is for reporting bugs and issues with GATK.

    You can read more about our forum guidelines and the topics here: Forum Guidelines.



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    Genevieve Brandt (she/her)

    Hi jorgez,

    Could you clarify what you mean by major constituent mtDNA? 

    To separate heteroplasmic from non-heteroplasmic DNA you can filter using AF. Heteroplasmic might not necessarily be 1.0 but the AF value will give you good information. The MTLowHeteroplasmyFilterTool is not best for this case.

    Hope this helps!


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