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Error in PlotGenotypingResults

archananrajaarchananraja MichiganMember
edited February 2015 in GenomeSTRiP

Hi
I was recently trying to plot one of my genotyped site using PlotGenotypingResults and get the below error.
Error in expected.data[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 org.broadinstitute.sv.apps.PlotGenotypingResults \
-site DEL_P0399_1 \
-O out.pdf \
-auxFilePrefix P0002 \
-partitionMapFile partition.genotypes.map.dat

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

Thanks,
Ar

Best Answer

  • bhandsakerbhandsaker ✭✭✭✭
    Accepted Answer

    Could you send me the input files for this variant? You can just extract the lines for DEL_P0399_1 if you want.
    Is there a reason you used -auxFilePrefix and -partitionMapFile instead of just using -runDirectory (which would be more typical)?

Answers

  • bhandsakerbhandsaker Member, Broadie ✭✭✭✭
    Accepted Answer

    Could you send me the input files for this variant? You can just extract the lines for DEL_P0399_1 if you want.
    Is there a reason you used -auxFilePrefix and -partitionMapFile instead of just using -runDirectory (which would be more typical)?

  • archananrajaarchananraja MichiganMember

    Hi ,
    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

    test1.genotypes.conf.dat

    DEL_P0026_1 1 25158687 25158688 25161531 25161532 5.70

    test1.genotypes.counts.dat
    DEL_P0026_1 5.0

    test1.genotypes.expected.dat

    DEL_P0026_1 28.82262295252939

    test1.genotypes.gmm.dat

    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

    test1.genotypes.gts.dat
    DEL_P0026_1 1 25158687 25158688 25161531 25161532 0

    test1.genotypes.norm.dat
    DEL_P0026_1 2842 317

    test1.genotypes.paircounts.dat
    DEL_P0026_1 20

    Let me know if you need anything else.

    Thank you very much for the help.

    Thanks,
    Ar

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