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# Haplotype Caller giving error in chrUn_gl000225 region

Posts: 5Member

Hi, We have used HaplotypeCaller for calling our whole genome sequencing data using hg19. Till now it called perfectly on every other chromosomes. But its giving an error message in chrUn_gl000225 region. I am uploading the error message.

##### ERROR stack trace

java.lang.NullPointerException at org.broadinstitute.sting.gatk.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods(PairHMMLikelihoodCalculationEngine.java:425) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods(PairHMMLikelihoodCalculationEngine.java:399) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.calculateGLsForThisEvent(GenotypingEngine.java:340) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.assignGenotypeLikelihoods(GenotypingEngine.java:207) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:837) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:141) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:708) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:704) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603) at java.lang.Thread.run(Thread.java:722)

Thanks, Mayukh

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