HaplotypeCaller error: Somehow the requested coordinate is not covered by the read

I am attempting to use the HaplotypeCaller to call indels and SNPs in genomes from the Illumina Platinum Genomes pedigree (http://www.illumina.com/platinumgenomes/). I did these steps before running haplotype caller:

  • alignment with BWA mem
  • mark duplicates with Picard
  • Indel realignment

I am now trying to run haplotype caller (version 3.2-2-gec30cee) with the realigned BAM files and am getting the following error:

##### ERROR stack trace
org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Somehow the requested coordinate is not covered by the read. Alignment 10357 | 86M15H
at org.broadinstitute.gatk.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:573)
at org.broadinstitute.gatk.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinate(ReadUtils.java:429)
at org.broadinstitute.gatk.utils.sam.ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(ReadUtils.java:425)
at org.broadinstitute.gatk.tools.walkers.annotator.BaseQualityRankSumTest.getElementForRead(BaseQualityRankSumTest.java:76)
at org.broadinstitute.gatk.tools.walkers.annotator.RankSumTest.getElementForRead(RankSumTest.java:200)
at org.broadinstitute.gatk.tools.walkers.annotator.RankSumTest.fillQualsFromLikelihoodMap(RankSumTest.java:179)
at org.broadinstitute.gatk.tools.walkers.annotator.RankSumTest.annotate(RankSumTest.java:102)
at org.broadinstitute.gatk.tools.walkers.annotator.interfaces.InfoFieldAnnotation.annotate(InfoFieldAnnotation.java:49)
at org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine.annotateContextForActiveRegion(VariantAnnotatorEngine.java:217)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.assignGenotypeLikelihoods(HaplotypeCallerGenotypingEngine.java:265)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:941)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:218)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:708)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:704)
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:273)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:78)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:314)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:107)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.2-2-gec30cee):
##### 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 http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Somehow the requested coordinate is not covered by the read. Alignment 10357 | 86M15H
##### ERROR ------------------------------------------------------------------------------------------

Notably, I don’t get this error when analyzing the same BAMs with UnifiedGenotyper. I have isolated a BAM file with ~1300 reads that can recreate the problem but couldn’t narrow it down further. The command I used is:

java -jar GenomeAnalysisTK.jar \
 -T HaplotypeCaller  \
 -R Homo_sapiens_assembly19_withchr.fasta \
 -I del.bam \
 -o del.hc.vcf \
 --output_mode EMIT_ALL_SITES

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