Tagged with #nullpointerexception
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I am following the GATK best practices workflow on Linux. I am using chr21.fa as reference from NCBI and .vcf files are taken from resource bundle and dbsnp.vcf is from NCBI. I am working on the VariantRecalibrator step. It gives me NullPointerException. I am attaching the console error that I have got which contains the command also and raw_variants.vcf which is generated in previous step by HaplotypeCaller tool in txt format. Please let me know what can be the issue.

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java.lang.NullPointerException at org.broadinstitute.sting.gatk.walkers.haplotypecaller.LikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods(LikelihoodCalculationEngine.java:379) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.LikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods(LikelihoodCalculationEngine.java:353) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.calculateGLsForThisEvent(GenotypingEngine.java:338) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.assignGenotypeLikelihoods(GenotypingEngine.java:205) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:778) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:140) 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.run(FutureTask.java:262) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:724)

Program Args: -nct 5 -T HaplotypeCaller -R ../ref/ref.fa -L chr10 -I <48 bam files> -o chr10.raw.vcf