If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Error in PlotGenotypingResults

archananrajaarchananraja MichiganMember


I had posted the same question before and you had asked for some addiational details. My post was tagged as answered by mistake.

I was recently trying to plot one of my genotyped site using PlotGenotypingResults and get the below error.
Error in[cnp, samples] : incorrect number of dimensions
Calls: main ... plotCnps -> plotSites -> plotCnpInternal -> asNumericInf

The command I ran is below :

java -Xmx4g -cp ${SV_DIR}/lib/SVToolkit.jar:${SV_DIR}/lib/gatk/GenomeAnalysisTK.jar \
-site DEL_P0399_1 \
-O out.pdf \
-auxFilePrefix P0002 \

The problem is in line 128 of the plot_cnps.R script where prints a value instead of a table in my case. It would be great if you can help me resolve this issue.



  • archananrajaarchananraja MichiganMember

    Thank you very much for the prompt reply.
    I tried executing the script with just the run directory and get the same error.

    Below are the example files
    DEL_P0026_1 1 25158687 25158688 25161531 25161532 5.70
    DEL_P0026_1 5.0
    DEL_P0026_1 28.82262295252939
    DEL_P0026_1 317 3 -3.028377 0.999997300694988,2.6993050030309E-6,8.54379040930724E-15 0.0,0.173474842744501,0.346949685489003 0.867371875160335,4.33685937580167,8.67371875160335
    DEL_P0026_1 1 25158687 25158688 25161531 25161532 0
    DEL_P0026_1 2842 317
    DEL_P0026_1 20
    Let me know if you need anything else.
    Thank you very much for the help.
Sign In or Register to comment.