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

(Notebook) Intro to using Mutect2 for somatic data Follow


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    My sample is WGS FFPE (tumor matched with normal tissue). I would like to add "Read Orientation Artifacts Workflow" to this workflow.

    How do I do it? Could you please add some hands-on script in this document?

    I checked this document (, but not sure.



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    I have an another question.

    For GetPileupSummaries step, can I specify normal.bam files separately like this?:

    gatk GetPileupSummaries \
       -I normal1.bam \
    -I normal2.bam \
    -I normal3.bam \ -V gnomad.vcf.gz \ -L common_snps.interval_list \ -O normal.pileups.table


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    Rafael Viana

    Very nice article.
    I just have 2 questions.

    1- Once you filter your variants and have the PASS flag.
        Is there a tool to remove the ones without the PASS flag?

    2- Here you get the differences between 2 samples.
        Lets say you have a suspect variant in your healthy sample, and you expect to find it in the sick sample
        Is it possible to check the samples similarities?

    Kind regards

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