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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

Haplotype caller variant frequency

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    Genevieve Brandt (she/her)

    Hi zgtman,

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

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

    Best,

    Genevieve

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    zgtman

    Dear Genevieve,

    thank ou for moving my post - please can you send me a link to this post? I can not find Community Discussion..

    Best,

    Petr.

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    Genevieve Brandt (she/her)

    Hi zgtman,

    I wanted to update you that I am looking closely into your request. Unfortunately, HaplotypeCaller is going to struggle to detect variants at such low frequencies so there are no easy arguments you can use to detect these variants. 

    In the past, some users have used Mutect2 to call these low frequency germline events using special parameters in Mutect2. I am currently looking into how other users have done this and I will update you when I have more information.

    Best,

    Genevieve

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    Genevieve Brandt (she/her)

    Hi zgtman,

    I followed up with our Mutect2 developer to determine the best way for you to proceed. And yes, they also recommended that using Mutect2 would be the best way for calling these mosaic events, since the signatures for calling mosaic events are similar to the signatures for calling somatic events.

    You can run Mutect2 with default parameters. We would recommend for best results to use a matched normal, which for your case would be another tissue sample that does not have the mosaic event, like a blood sample.

    Please let me know if you have any follow up questions.

    Best,

    Genevieve

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