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

How can i remove chr_Un* from somatic cnv plots?



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    Genevieve Brandt (she/her)

    Hi sahuno, I am looking at this tutorial and I found a note that may help you with this:

    Section 8: Plot modeled copy ratio and allelic fraction segments with PlotModeledSegments

    Comments on select parameters - The tutorial provides the --sequence-dictionary that matches the GRCh38 reference used in mapping - To omit alternate and decoy contigs from the plots, the tutorial adjusts the --minimum-contig-length from the default value of 1,000,000 to 46,709,983, the length of the smallest of GRCh38's primary assembly contigs.

    Also below that are options for interactively visualizing the data since the option -L for intervals is not available.

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    Genevieve-Brandt-she-her thanks!

    that was helpful!



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