I am trying to run GATK 3.7 for variant calling and I keep getting this error. Any comments about what this error is? Thanks!
ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions https://software.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: VC alleles [A*, C, ] not a strict subset of per read allele map alleles []
ERROR ------------------------------------------------------------------------------------------
INFO 11:51:27,856 ProgressMeter - 1:12907532 9.48476025E8 2.5 m 0.0 s 0.9% 4.7 h 4.7 h
INFO 11:51:41,137 ProgressMeter - 1:10043261 4.51176908E8 60.0 s 0.0 s 0.6% 2.7 h 2.7 h
INFO 11:51:57,857 ProgressMeter - 1:16360411 1.354980846E9 3.0 m 0.0 s 1.1% 4.7 h 4.7 h
WARN 11:52:04,691 AnnotationUtils - Annotation will not be calculated, genotype is not called
WARN 11:52:04,735 AnnotationUtils - Annotation will not be calculated, genotype is not called
ERROR --
ERROR stack trace
java.lang.IllegalStateException: VC alleles [A, ATCT*, ] not a strict subset of per read allele map alleles []
at org.broadinstitute.gatk.utils.sam.AlignmentUtils.countBasesAtPileupPosition(AlignmentUtils.java:1408)
at org.broadinstitute.gatk.tools.walkers.annotator.BaseCounts.getBaseCounts(BaseCounts.java:93)
at org.broadinstitute.gatk.tools.walkers.annotator.BaseCounts.annotate(BaseCounts.java:78)
at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine.annotateContextForActiveRegion(VariantAnnotatorEngine.java:315)
at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine.annotateContextForActiveRegion(VariantAnnotatorEngine.java:260)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.annotateCall(HaplotypeCallerGenotypingEngine.java:328)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.assignGenotypeLikelihoods(HaplotypeCallerGenotypingEngine.java:290)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:962)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:250)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:709)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:705)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:274)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:78)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:98)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:316)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)