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Error in VariantEval: ClassCastException

akiezunakiezun Posts: 17Member
edited September 2012 in Ask the GATK team

I'm on unstable v2.1-61-gde29ed5, Compiled 2012/08/23 16:03:06

I run VariantEval on the file below and get this:

java.lang.ClassCastException: java.util.ArrayList cannot be cast to java.lang.String
       at org.broadinstitute.sting.utils.variantcontext.CommonInfo.getAttributeAsInt(CommonInfo.java:212)
       at org.broadinstitute.sting.utils.variantcontext.VariantContext.getAttributeAsInt(VariantContext.java:600)
                at org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.AlleleCount.getRelevantStates(AlleleCount.java:50)
                at org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval.getEvaluationContexts(VariantEval.java:481)
                at org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval.map(VariantEval.java:409)
                at org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval.map(VariantEval.java:91)
                at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:65)
                at org.broadinstitute.sting.gatk.traversals.TraverseLoci.traverse(TraverseLoci.java:18)
                at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:72)
                at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:268)
                at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
                at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
                at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
                at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)`

The file is this (after header)

    #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  A3N     A4N     A5N     A6N     A8N     A9N     H10N    H15N    H17N    H26N    H27N    H32N    H52N    H53N   H54N     H55N    H56N    H57N    H58N    H61N    H62N    H6N     H7N
    1       901922  rs62639980      G       A,C     1332.23 PASS    AC=1,2;AF=6.849e-03,0.014;AN=146;BaseQRankSum=-3.705;DB;DP=2675;DS;Dels=0.00;FS=3.860;HaplotypeScore=1.6813;InbreedingCoeff=-0.0001;MLEAC=2,2;MLEAF=0.014,0.014;MQ=58.62;MQ0=1;MQRankSum=2.225;QD=7.84;ReadPosRankSum=3.761;SB=-5.136e+02;VQSLOD=3.9184;culprit=HaplotypeScore  GT:AD:DP:GQ:PL  0/0:1,0,0:59:99:0,178,2360,178,2360,2360        0/0:60,0,0:60:99:0,156,2055,156,2055,2055       0/0:60,0,0:60:99:0,160,2191,160,2191,2191       0/0:1,0,0:64:99:0,193,2516,193,2516,2516        0/0:1,0,0:47:99:0,141,1776,141,1776,1776        0/0:1,0,0:62:99:0,187,2480,187,2480,2480        0/0:59,1,0:60:99:0,119,1965,147,1968,1996       0/0:56,0,0:56:99:0,135,1857,135,1857,1857      0/0:1,0,0:57:99:0,172,2280,172,2280,2280 0/0:1,0,0:75:99:0,226,3000,226,3000,3000        0/0:8,0,0:71:99:0,214,2852,214,2852,2852        0/0:60,0,0:60:99:0,147,1942,147,1942,1942      0/0:47,0,0:47:99:0,123,1654,123,1654,1654        0/0:1,0,0:56:99:0,169,2240,169,2240,2240        0/0:1,0,0:55:99:0,166,2122,166,2122,2122        0/2:37,0,23:60:99:647,734,1844,0,1110,1050      0/0:1,0,0:71:99:0,214,2840,214,2840,2840        0/2:44,0,16:60:99:377,483,1801,0,1319,1277      0/0:57,0,0:57:99:0,141,1914,141,1914,1914       0/0:1,0,0:53:99:0,160,2154,160,2154,2154        0/0:1,0,0:74:99:0,223,3008,223,3008,3008        0/0:1,0,0:49:99:0,147,1960,147,1960,1960        0/0:1,0,0:76:99:0,229,2988,229,2988,2988`

The file was created by first calling my ~20 samples with 50 random samples from 1kg and then subsetting to my samples using SelectVariants.

Post edited by Geraldine_VdAuwera on
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