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GATK CalculateContamination (paired mode) - NaN value

I am applying the Mutect2 pipeline (GATK v4.1.2.0) to my WES data (tumor samples and their matched normal counterparts) to detect somatic mutations. However, for two patients, when I try to calculate the contamination, the result is NaN. As a consequence, after running FilterMutectCalls, the output file (mutect2.filtered.vcf) is empty. Here's the pipeline:

# Pileup table for the tumour sample
${GATK} GetPileupSummaries \
   -I ${BAM_TUM} \
   -V ${SNP1000G} \
   -O $OUT_FOLDER2/TUM.pileups.table

# Pileup table for the normal sample 
${GATK} GetPileupSummaries \
   -I ${BAM_NORM} \
   -V ${SNP1000G} \
   -O $OUT_FOLDER2/NORM.pileups.table

${GATK} CalculateContamination \
   -I $OUT_FOLDER2/TUM.pileups.table \
   -matched $OUT_FOLDER2/NORM.pileups.table \
   -O $OUT_FOLDER2/contamination.table
${GATK} Mutect2 \
   -R ${REFGENOME} \
   -I ${BAM_TUM} \
   -I ${BAM_NORM} \
   -normal COLO829BL \
   -tumor COLO829T \
   --germline-resource ${SNP1000G} \
   --panel-of-normals ${PON} \
   -O ${OUT_FOLDER2}/mutect2.vcf 

${GATK} FilterMutectCalls \
   -R ${REFGENOME} \
   -V ${OUT_FOLDER2}/mutect2.vcf \
   --contamination-table $OUT_FOLDER2/contamination.table \
   --min-allele-fraction 0.01 \
   -O ${OUT_FOLDER2}/mutect2.filtered.vcf

And here's the log file for the CalculateContamination command:

21:41:35.208 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Dec 15, 2025 9:42:35 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
21:42:35.569 INFO  CalculateContamination - ------------------------------------------------------------
21:42:35.570 INFO  CalculateContamination - The Genome Analysis Toolkit (GATK) v4.1.2.0
21:42:35.570 INFO  CalculateContamination - For support and documentation go to https://software.broadinstitute.org/gatk/
21:42:35.573 INFO  CalculateContamination - Executing as valentina@ped823 on Linux v3.10.0-957.1.3.el7.x86_64 amd64
21:42:35.573 INFO  CalculateContamination - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_92-b15
21:42:35.573 INFO  CalculateContamination - Start Date/Time: December 15, 2025 9:41:35 PM CET
21:42:35.573 INFO  CalculateContamination - ------------------------------------------------------------
21:42:35.573 INFO  CalculateContamination - ------------------------------------------------------------
21:42:35.576 INFO  CalculateContamination - HTSJDK Version: 2.19.0
21:42:35.576 INFO  CalculateContamination - Picard Version: 2.19.0
21:42:35.576 INFO  CalculateContamination - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:42:35.576 INFO  CalculateContamination - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:42:35.576 INFO  CalculateContamination - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:42:35.576 INFO  CalculateContamination - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:42:35.576 INFO  CalculateContamination - Deflater: IntelDeflater
21:42:35.576 INFO  CalculateContamination - Inflater: IntelInflater
21:42:35.576 INFO  CalculateContamination - GCS max retries/reopens: 20
21:42:35.576 INFO  CalculateContamination - Requester pays: disabled
21:42:35.576 INFO  CalculateContamination - Initializing engine
21:42:35.576 INFO  CalculateContamination - Done initializing engine
21:42:37.120 INFO  KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
21:42:37.228 INFO  KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
21:42:37.236 WARN  KernelSegmenter - Specified dimension of the kernel approximation (100) exceeds the number of data points (74) to segment; using all data points to calculate kernel matrix.
21:42:37.248 INFO  KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
21:42:37.274 INFO  KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
21:42:37.306 INFO  KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
21:42:37.345 INFO  KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
21:42:37.350 WARN  KernelSegmenter - Specified dimension of the kernel approximation (100) exceeds the number of data points (98) to segment; using all data points to calculate kernel matrix.
21:42:37.370 INFO  KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
21:42:37.411 INFO  KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
21:42:37.455 INFO  KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
21:42:37.493 INFO  KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
21:42:37.544 INFO  KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
21:42:37.568 INFO  KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
21:42:37.594 INFO  KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
21:42:37.627 INFO  KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
21:42:37.644 INFO  KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
21:42:37.666 INFO  KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
21:42:37.683 INFO  KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
21:42:37.696 INFO  KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
21:42:37.716 INFO  KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
21:42:37.732 INFO  KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
21:42:37.747 INFO  KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
21:42:37.762 INFO  KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
21:42:37.781 INFO  KernelSegmenter - Found 0 changepoints after applying the changepoint penalty.
21:42:45.164 INFO  CalculateContamination - Shutting down engine
[December 15, 2025 9:42:45 PM CET] org.broadinstitute.hellbender.tools.walkers.contamination.CalculateContamination done. Elapsed time: 1.17 minutes.
Runtime.totalMemory()=2444230656
Tool returned:
SUCCESS

While here's the FilterMutectCalls log:

Using GATK jar /opt/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar defined in environment variable GATK_LOCAL_JAR
Running:
  java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /opt/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar LearnReadOrientationModel -I f1r2.tar.gz -O oribias.tar.gz
23:18:23.401 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Dec 15, 2025 11:19:23 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
23:19:23.866 INFO  FilterMutectCalls - ------------------------------------------------------------
23:19:23.867 INFO  FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.1.2.0
23:19:23.867 INFO  FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
23:19:23.870 INFO  FilterMutectCalls - Executing as valentina@ped823 on Linux v3.10.0-957.1.3.el7.x86_64 amd64
23:19:23.871 INFO  FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_92-b15
23:19:23.871 INFO  FilterMutectCalls - Start Date/Time: December 15, 2025 11:18:23 PM CET
23:19:23.871 INFO  FilterMutectCalls - ------------------------------------------------------------
23:19:23.871 INFO  FilterMutectCalls - ------------------------------------------------------------
23:19:23.872 INFO  FilterMutectCalls - HTSJDK Version: 2.19.0
23:19:23.872 INFO  FilterMutectCalls - Picard Version: 2.19.0
23:19:23.872 INFO  FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:19:23.872 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:19:23.873 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:19:23.873 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:19:23.873 INFO  FilterMutectCalls - Deflater: IntelDeflater
23:19:23.873 INFO  FilterMutectCalls - Inflater: IntelInflater
23:19:23.873 INFO  FilterMutectCalls - GCS max retries/reopens: 20
23:19:23.873 INFO  FilterMutectCalls - Requester pays: disabled
23:19:23.873 INFO  FilterMutectCalls - Initializing engine
23:19:24.274 INFO  FeatureManager - Using codec VCFCodec to read file file:///data/PROJECTS/LIVIA/GIST_AIRC/GIST_AIRC_111225/23T072455/mutect/mutect2.vcf
23:19:24.307 INFO  FilterMutectCalls - Done initializing engine
23:19:24.385 INFO  IOUtils - Extracting data from archive: file:///data/PROJECTS/LIVIA/GIST_AIRC/GIST_AIRC_111225/23T072455/mutect/oribias.tar.gz
23:19:24.391 INFO  IOUtils - Extracting file: ./15_S11.orientation_priors
23:19:24.423 INFO  ProgressMeter - Starting traversal
23:19:24.424 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
23:19:24.424 INFO  FilterMutectCalls - Starting pass 0 through the variants
23:19:24.459 INFO  FilterMutectCalls - Shutting down engine
[December 15, 2025 11:19:24 PM CET] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 1.02 minutes.
Runtime.totalMemory()=1847590912
java.lang.IllegalArgumentException: log10p: Log10-probability must be 0 or less
at org.broadinstitute.hellbender.utils.Utils.validateArg(Utils.java:724)
at org.broadinstitute.hellbender.utils.MathUtils.log10BinomialProbability(MathUtils.java:917)
at org.broadinstitute.hellbender.utils.MathUtils.binomialProbability(MathUtils.java:910)
at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ContaminationFilter.calculateErrorProbability(ContaminationFilter.java:56)
at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2VariantFilter.errorProbability(Mutect2VariantFilter.java:15)
at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ErrorProbabilities.lambda$new$1(ErrorProbabilities.java:19)
at java.util.stream.Collectors.lambda$toMap$58(Collectors.java:1321)
at java.util.stream.ReduceOps$3ReducingSink.accept(ReduceOps.java:169)
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1374)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.ErrorProbabilities.<init>(ErrorProbabilities.java:19)
at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.Mutect2FilteringEngine.accumulateData(Mutect2FilteringEngine.java:141)
at org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls.nthPassApply(FilterMutectCalls.java:140)
at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.lambda$traverse$0(MultiplePassVariantWalker.java:40)
at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.lambda$traverseVariants$1(MultiplePassVariantWalker.java:77)
at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.traverseVariants(MultiplePassVariantWalker.java:75)
at org.broadinstitute.hellbender.engine.MultiplePassVariantWalker.traverse(MultiplePassVariantWalker.java:40)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1039)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
at org.broadinstitute.hellbender.Main.main(Main.java:291)

Do you have any idea why this might be happening, and do you have any suggestions on how to address or overcome this issue?

Thanks in advance

gatk calculatecontamination mutect2
• 724 views • link
written by Livia • Livia

it looks like like one of the probabilities are incorrect, check the VCF files, maybe something stands out right away

• 0 views • link
written by Istvan Albert Istvan Albert

Thank you for the reply. What should I look for in the VCF files? Do you have any specific advice?

• 0 views • link
written by Livia • Livia

0 answers

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