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

PlotModeledSegments Follow

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    Alexandre Mondaini

    Hello there,

    I'm experiencing some plotting issues with this tool, mostly the right side of the image is totally squished and I can't visualize the high number chromosomes.

    This is the script I used to make the image:

    gatk --java-options "-Xmx6000m" PlotModeledSegments \
        --denoised-copy-ratios \
        --allelic-counts \
        --segments \
        --sequence-dictionary Homo_sapiens_assembly38.dict \
        --minimum-contig-length 1000000 \
        --maximum-copy-ratio 4.0 \
        --point-size-copy-ratio 0.2 \
        --point-size-allele-fraction 0.4 \
        --output out \
    And this is the image:
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