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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    Ashi

    Hi,

    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 (https://gatk.broadinstitute.org/hc/en-us/articles/360035531132), but not sure.

     

    Thanks!

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    Ashi

    Hi,

    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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