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.