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Variant Recalibration generates NullPointerException at VariantRecalibratorEngine.generateModel

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.


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Jitendra,

    The error is occurring because you are running on an extremely small set of variant calls. The variant recalibrator cannot build a proper model with so few variants. I will see if we can provide better error handling and a more informative error message in the future, but in any case VQSR will not work on such a small dataset. I assume you are doing this for testing purposes, but please be aware that it is simply not possible to do small-scale testing of VQSR.

  • shazlyshazly EgyptMember

    Hi Geraldine,

    I'm getting the same error although my variant calls file is 3.2M, Is this considered a small file too or else do you have any suggestions why i'm getting this error in my case?

    And This the command i run:

    java -Xmx4g -jar GenomeAnalysisTK.jar -T VariantRecalibrator -R ~/bwa_references/human_g1k_v37.fasta -input ~/simplex/ngs_test/snp_calling/aln.haplotyper.raw.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=8.0 ~/bundle/current/dbsnp_137.b37.vcf -resource:hapmap,VCF,known=false,training=true,truth=true,prior=15.0 ~/bundle/current/hapmap_3.3.b37.vcf -resource:omni,VCF,known=false,training=true,truth=false,prior=12.0 ~/bundle/current/1000G_omni2.5.b37.vcf -an QD -an MQRankSum -an ReadPosRankSum -recalFile ~/ngs_test/snp_recal/aln.snp.recal -tranche 100 -tranche 99.9 -tranche 99.0 -tranche 90 -tranchesFile ~/ngs_test/snp_recal/aln.snp.tranches -rscriptFile ~/ngs_test/snp_recal/aln.snp.plots.R -mode SNP



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi @shazly,

    That's right, based on the filesize it's likely that you don't have enough variants for recalibration. See the solutions proposed in the documentation for dealing with this problem.

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