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

DepthOfCoverage (BETA) Follow


  • Avatar
    Chet Revers

    A DEVELOPER ERROR has occurred: -ct is not a recognized option

    but the -ct option is provided in the "Usage example" above 

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    Seunghun Han


    I was using DepthOfCoverage from GATK-3.7 before, and 
    after I updated it to the one from latest GATK, I'm getting individual gene level 
    summary for each gene transcript for a gene when I use the -gene-list option. 
    In the previous version, the gene level summary output produced single row per gene.
    Is there an option I need to add on top of -gene-list to get aggregate gene level summary?

    This is how I run DoC -
    gatk --java-options "-Xmx16G" DepthOfCoverage -R ${refFasta} \
    -O ${sampleName} --omit-depth-output-at-each-base true \
    -pt sample -gene-list ${geneList} -I cramfile.cram \
    -L ${intervalList} --min-base-quality ${minBaseQuality}

    And I'm using a gene list generate by following this instruction -

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