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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

Not generating denoisedLimit4.png with PlotModeledSegments

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    Pamela Bretscher

    Hi Hanyin Wang,

    Thank you for writing in to the forum. Are you seeing any issue with the output of PlotModeledSegments? I see your command for PlotModeledSegments but your output of PlotDenoisedCopyRatios. Could you post the command that you ran for PlotDenoisedCopyRatios given that you are experiencing an issue with the output from this tool?

    Kind regards,

    Pamela

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    Hanyin Wang

    Thanks for the kind reply Pamela!

    I am so sorry I meant to say the issue is with PlotDenoisedCopyRatios. No issue with PlotModeledSegments. Would be happy to change the question if there's a way.

    Here's my command for PlotDenoisedCopyRatios:

    gatk PlotDenoisedCopyRatios \
        --standardized-copy-ratios {input.standardized} \
        --denoised-copy-ratios {input.denoised} \
        --sequence-dictionary {config[reference_dict]} \
        --minimum-contig-length {config[min_contig_len]} \
        --output {params.outputdir} \
        --output-prefix {params.outputprefix} 

    Best,

    Hanyin

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    Pamela Bretscher

    Hi Hanyin Wang,

    Thank you for sharing the command and no worries about changing the question! The somatic CNV pipeline is actually out of date so PlotDenoisedCopyRatios works a little bit differently now. The denoisedLimit4.png file is no longer generated and the denoised.png file automatically restricts the copy ratio to a value of 4, which you should see reflected in this file. If you would like to change the default max copy ratio, you can specify --maximum-copy-ratio when running the tool. I hope this clarifies the results you are getting, please let me know if you have any additional questions.

    Kind regards,

    Pamela

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    Hanyin Wang

    This is tremendously helpful! Thank you so much Pamela.

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