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FilterMutectCalls error :"there is no such column: sample"

Hi,

I've been following the best practice for tumor somatic mutation calling.

Everything runs like a charm until FilterMutectCalls which keeps throwing a java error:
"java.lang.IllegalArgumentException: there is no such column: sample"

This is WES (on PDX) with paired normal sample, using GATK4.1.
ValidateVariants went perfectly well.

Any idea? Am I missing something?

Thank you in advance.

Kind regards.

Here is the FilterMutectCalls cmd and log:

  java -jar gatk-package-4.1.0.0-local.jar FilterMutectCalls -V Sample_PDAC_JIA_HS_003T_DNA.vcf --contamination-table Sample_PDAC_JIA_HS_003T_DNA_calculatecontamination.table -O Sample_PDAC_JIA_HS_003T_DNA_oncefiltered.vcf
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 /datacit/03_TOOLS/SeqTools/GATK/gatk-4.1.0.0/gatk-package-4.1.0.0-local.jar FilterMutectCalls -V Sample_PDAC_JIA_HS_003T_DNA.vcf --contamination-table Sample_PDAC_JIA_HS_003T_DNA_calculatecontamination.table -O Sample_PDAC_JIA_HS_003T_DNA_oncefiltered.vcf
21:20:09.207 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/datacit/03_TOOLS/SeqTools/GATK/gatk-4.1.0.0/gatk-package-4.1.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
21:20:19.585 INFO  FilterMutectCalls - ------------------------------------------------------------
21:20:19.586 INFO  FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.1.0.0
21:20:19.586 INFO  FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
21:20:19.587 INFO  FilterMutectCalls - Executing as [email protected] on Linux v3.10.0-693.17.1.el7.x86_64 amd64
21:20:19.587 INFO  FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_191-b12
21:20:19.588 INFO  FilterMutectCalls - Start Date/Time: 27 février 2019 21:20:09 CET
21:20:19.589 INFO  FilterMutectCalls - ------------------------------------------------------------
21:20:19.589 INFO  FilterMutectCalls - ------------------------------------------------------------
21:20:19.590 INFO  FilterMutectCalls - HTSJDK Version: 2.18.2
21:20:19.591 INFO  FilterMutectCalls - Picard Version: 2.18.25
21:20:19.591 INFO  FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
21:20:19.591 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
21:20:19.592 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
21:20:19.592 INFO  FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
21:20:19.593 INFO  FilterMutectCalls - Deflater: IntelDeflater
21:20:19.593 INFO  FilterMutectCalls - Inflater: IntelInflater
21:20:19.593 INFO  FilterMutectCalls - GCS max retries/reopens: 20
21:20:19.594 INFO  FilterMutectCalls - Requester pays: disabled
21:20:19.594 INFO  FilterMutectCalls - Initializing engine
21:20:19.941 INFO  FeatureManager - Using codec VCFCodec to read file file:///datacompute/pacaomics/04_Processed/Variant_calling/Mutect2/Sample_PDAC_JIA_HS_003T_DNA/Sample_PDAC_JIA_HS_003T_DNA.vcf
21:20:20.028 INFO  FilterMutectCalls - Done initializing engine
21:20:20.131 INFO  FilterMutectCalls - Shutting down engine
[27 février 2019 21:20:20 CET] org.broadinstitute.hellbender.tools.walkers.mutect.FilterMutectCalls done. Elapsed time: 0.18 minutes.
Runtime.totalMemory()=2175795200
java.lang.IllegalArgumentException: there is no such column: sample
    at org.broadinstitute.hellbender.utils.tsv.DataLine.columnIndex(DataLine.java:431)
    at org.broadinstitute.hellbender.utils.tsv.DataLine.get(DataLine.java:400)
    at org.broadinstitute.hellbender.utils.tsv.DataLine.get(DataLine.java:529)
[...]

Here's the mutect2 cmd :

 java gatk-package-4.1.0.0-local.jar Mutect2 -R ensembl91.GRC38_hgmmu_chrename.fa -I Sample_PDAC_JIA_HS_003T_DNA.nochrFilt.reord.sorted.dedup.recal.bam -I Sample_PDAC_JIA_HS_003N_DNA.nochrFilt.reord.sorted.dedup.recal.bam -tumor Sample_PDAC_JIA_HS_003T_DNA -normal Sample_PDAC_JIA_HS_003N_DNA -pon mutect2_pon.vcf --germline-resource somatic-hg38_af-only-gnomad.hg38_withoutContig_hschr.vcf --af-of-alleles-not-in-resource 0.0000025 --disable-read-filter MateOnSameContigOrNoMappedMateReadFilter -O Sample_PDAC_JIA_HS_003T_DNA.vcf -bamout Sample_PDAC_JIA_HS_003T_DNA_Sample_PDAC_JIA_HS_003N_DNA.bam --tmp-dir /datacompute/pacaomics/tmpdir

Best Answers

  • renicollerenicolle Curie
    Accepted Answer

    Thanks for the answer.

    It was actually due to incompatibility between previous GATK "CalculateContamination" that did not give sample names to rows in the contamination table.

    So entirely my fault, not using the same version of GATK for filtering mutation and calculating contamination.

    Very sorry to have bothered you for this.

    Thank you so much for the tools and support.

Answers

  • renicollerenicolle CurieMember
    Accepted Answer

    Thanks for the answer.

    It was actually due to incompatibility between previous GATK "CalculateContamination" that did not give sample names to rows in the contamination table.

    So entirely my fault, not using the same version of GATK for filtering mutation and calculating contamination.

    Very sorry to have bothered you for this.

    Thank you so much for the tools and support.

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