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

Mutect2 - using a primary tumour sample instead of a normal sample

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    Genevieve Brandt (she/her)

    Hi Thomas Bradley,

    Your first question: Depending on the purity of your primary tumor sample and the allele fractions that you get, you might see the germline filter in addition to the normal_artifact filter. 

    Your second question: We wouldn't recommend messing around with the normal-lod parameter.

    Hope this helps!

    If other GATK users have tried this use case, feel free to chime in with what worked for you!

    Genevieve

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    Thomas Bradley

    Hi Genevieve Brandt (she/her),

    Thank you very much for your response.

    Ah yes, I forgot about this - some of the variants in the primary tumour will also be likely classed as germline.

    I agree, I don't want to touch the normal-lod parameter unless I am certain I know what the effects of that will be.

    As I am still unsure, I am postponing this proposed type of analysis for now (i.e. using mutect2 to look at the same cancer pre- and post-treatment), but I am also interested to hear if others have attempted this type of analysis with mutect2 and what their findings are

    Thank you,
    Thomas 

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    Jaime Alvarez Benayas

    Hi Thomas Bradley, I am doing a similar kind of analysis as what you described (pseudonormal = tumor state 1, tumor = tumor state 2). Did you manage to run successfully the analysis you were describing?

    I find most of my variants (~84%) are categorized with "normal_artifact", I ran with default parameters, but I am also interested in seeing where the proportion of alternative allele varies significantly beween pseudonormal and tumor. 

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