GATK4 VariantAnnotator deletes variants
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Entering edit mode
4 months ago
ManuelDB ▴ 110

I am using VariantAnnotator gatk:4.1.3.0 without success and not clear error message is shown. However, same code in GATK3 works fine. I show the code with both versions

 apptainer exec --bind /mnt:/mnt docker://broadinstitute/gatk:4.1.3.0 \
          /gatk/gatk IndexFeatureFile \
          -F "240605_M00321_0177_000000000-GLNFM_1109026765.vcf"

apptainer exec --bind /mnt:/mnt docker://broadinstitute/gatk:4.1.3.0 \
          /gatk/gatk VariantAnnotator  \
            -R $bwarefgenomepath \
            -V "1109026765/240605_M00321_0177_000000000-GLNFM_1109026765.vcf" \
            -I "1109026765/240605_M00321_0177_000000000-GLNFM_1109026765.bam" \
            -O "1109026765/240605_M00321_0177_000000000-GLNFM_1109026765_anno_GATK4.vcf" \
            -L "$ampliconscoordenatesbed" \
            -A BaseQualityRankSumTest \
            -A ReadPosRankSumTest \
            --verbosity DEBUG


tail  "1109026765/240605_M00321_0177_000000000-GLNFM_1109026765_anno.vcf"

apptainer exec --bind /mnt:/mnt docker://pegi3s/gatk-3:3.8-0 java \
        -Xmx4G -jar /opt/GenomeAnalysisTK.jar \
        -T VariantAnnotator \
        -R $bwarefgenomepath \
        -I "1109026765/240605_M00321_0177_000000000-GLNFM_1109026765.bam" \
        -V "1109026765/240605_M00321_0177_000000000-GLNFM_1109026765.vcf" \
        -L "$ampliconscoordenatesbed"  \
        -o "1109026765/240605_M00321_0177_000000000-GLNFM_1109026765_anno_GATK3.vcf" \
        -A BaseQualityRankSumTest \
        -A ReadPosRankSumTest \
        -dt NONE

tail "1109026765/240605_M00321_0177_000000000-GLNFM_1109026765_anno_GATK3.vcf"

1109026765/240605_M00321_0177_000000000-GLNFM_1109026765.vcf has 1 variant 1109026765/240605_M00321_0177_000000000-GLNFM_1109026765_anno_GATK4.vcf has 0 variant 1109026765/240605_M00321_0177_000000000-GLNFM_1109026765_anno_GATK3.vcf has 1 variant

I have tried with different GATK4 versions. I Have tried with gatk:4.6.0.0. Same results

The info from the tool

 Using GATK jar /gatk/gatk-package-4.6.0.0-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 /gatk/gatk-package-4.6.0.0-local.jar VariantAnnotator -R /mnt/data1/db/gcp-public-data--broad-references/hg38/v0/GIABv1mask/Homo_sapiens_assembly38.GIABv1mask.fasta -V /mnt/scratch1/projects/SSrep/240605_M00321_0177_000000000-GLNFM-light/1109026765/240605_M00321_0177_000000000-GLNFM_1109026765.vcf -I /mnt/scratch1/projects/SSrep/240605_M00321_0177_000000000-GLNFM-light/1109026765/240605_M00321_0177_000000000-GLNFM_1109026765.bam -O /mnt/scratch1/projects/SSrep/240605_M00321_0177_000000000-GLNFM-light/1109026765/240605_M00321_0177_000000000-GLNFM_1109026765_anno.vcf -L /home/dominm/SomaticPipeline/ref_files/bed_files/SSrep/SSrep_amplicons_v4.1.bed -A BaseQualityRankSumTest -A ReadPosRankSumTest --verbosity DEBUG
08:35:33.263 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.6.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
08:35:33.299 DEBUG NativeLibraryLoader - Extracting libgkl_compression.so to /tmp/libgkl_compression6022680971929891226.so
08:35:33.461 INFO  VariantAnnotator - ------------------------------------------------------------
08:35:33.464 INFO  VariantAnnotator - The Genome Analysis Toolkit (GATK) v4.6.0.0
08:35:33.464 INFO  VariantAnnotator - For support and documentation go to https://software.broadinstitute.org/gatk/
08:35:33.465 INFO  VariantAnnotator - Executing as dominm@wglsbi01 on Linux v4.18.0-553.8.1.el8_10.x86_64 amd64
08:35:33.465 INFO  VariantAnnotator - Java runtime: OpenJDK 64-Bit Server VM v17.0.9+9-Ubuntu-122.04
08:35:33.465 INFO  VariantAnnotator - Start Date/Time: July 23, 2024 at 8:35:33 AM GMT
08:35:33.465 INFO  VariantAnnotator - ------------------------------------------------------------
08:35:33.465 INFO  VariantAnnotator - ------------------------------------------------------------
08:35:33.465 INFO  VariantAnnotator - HTSJDK Version: 4.1.1
08:35:33.466 INFO  VariantAnnotator - Picard Version: 3.2.0
08:35:33.466 INFO  VariantAnnotator - Built for Spark Version: 3.5.0
08:35:33.467 INFO  VariantAnnotator - HTSJDK Defaults.BUFFER_SIZE : 131072
08:35:33.467 INFO  VariantAnnotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
08:35:33.467 INFO  VariantAnnotator - HTSJDK Defaults.CREATE_INDEX : false
08:35:33.467 INFO  VariantAnnotator - HTSJDK Defaults.CREATE_MD5 : false
08:35:33.467 INFO  VariantAnnotator - HTSJDK Defaults.CUSTOM_READER_FACTORY :
08:35:33.467 INFO  VariantAnnotator - HTSJDK Defaults.DISABLE_SNAPPY_COMPRESSOR : false
08:35:33.467 INFO  VariantAnnotator - HTSJDK Defaults.EBI_REFERENCE_SERVICE_URL_MASK : https://www.ebi.ac.uk/ena/cram/md5/%s
08:35:33.467 INFO  VariantAnnotator - HTSJDK Defaults.NON_ZERO_BUFFER_SIZE : 131072
08:35:33.467 INFO  VariantAnnotator - HTSJDK Defaults.REFERENCE_FASTA : null
08:35:33.467 INFO  VariantAnnotator - HTSJDK Defaults.SAM_FLAG_FIELD_FORMAT : DECIMAL
08:35:33.467 INFO  VariantAnnotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
08:35:33.467 INFO  VariantAnnotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
08:35:33.467 INFO  VariantAnnotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
08:35:33.467 INFO  VariantAnnotator - HTSJDK Defaults.USE_CRAM_REF_DOWNLOAD : false
08:35:33.468 DEBUG ConfigFactory - Configuration file values:
08:35:33.469 DEBUG ConfigFactory -      gcsMaxRetries = 20
08:35:33.469 DEBUG ConfigFactory -      gcsProjectForRequesterPays =
08:35:33.469 DEBUG ConfigFactory -      gatk_stacktrace_on_user_exception = false
08:35:33.469 DEBUG ConfigFactory -      samjdk.use_async_io_read_samtools = false
08:35:33.469 DEBUG ConfigFactory -      samjdk.use_async_io_write_samtools = true
08:35:33.469 DEBUG ConfigFactory -      samjdk.use_async_io_write_tribble = false
08:35:33.469 DEBUG ConfigFactory -      samjdk.compression_level = 2
08:35:33.469 DEBUG ConfigFactory -      spark.kryoserializer.buffer.max = 512m
08:35:33.470 DEBUG ConfigFactory -      spark.driver.maxResultSize = 0
08:35:33.470 DEBUG ConfigFactory -      spark.driver.userClassPathFirst = true
08:35:33.470 DEBUG ConfigFactory -      spark.io.compression.codec = lzf
08:35:33.470 DEBUG ConfigFactory -      spark.executor.memoryOverhead = 600
08:35:33.470 DEBUG ConfigFactory -      spark.driver.extraJavaOptions =
08:35:33.470 DEBUG ConfigFactory -      spark.executor.extraJavaOptions =
08:35:33.470 DEBUG ConfigFactory -      codec_packages = [htsjdk.variant, htsjdk.tribble, org.broadinstitute.hellbender.utils.codecs]
08:35:33.470 DEBUG ConfigFactory -      read_filter_packages = [org.broadinstitute.hellbender.engine.filters]
08:35:33.470 DEBUG ConfigFactory -      annotation_packages = [org.broadinstitute.hellbender.tools.walkers.annotator]
08:35:33.470 DEBUG ConfigFactory -      cloudPrefetchBuffer = 40
08:35:33.470 DEBUG ConfigFactory -      cloudIndexPrefetchBuffer = -1
08:35:33.470 DEBUG ConfigFactory -      createOutputBamIndex = true
08:35:33.470 INFO  VariantAnnotator - Deflater: IntelDeflater
08:35:33.470 INFO  VariantAnnotator - Inflater: IntelInflater
08:35:33.470 INFO  VariantAnnotator - GCS max retries/reopens: 20
08:35:33.470 INFO  VariantAnnotator - Requester pays: disabled
08:35:33.471 INFO  VariantAnnotator - Initializing engine
08:35:33.696 INFO  FeatureManager - Using codec VCFCodec to read file file:///mnt/scratch1/projects/SSrep/240605_M00321_0177_000000000-GLNFM-light/1109026765/240605_M00321_0177_000000000-GLNFM_1109026765.vcf
08:35:33.716 DEBUG GenomeLocParser - Prepared reference sequence contig dictionary
08:35:33.717 DEBUG GenomeLocParser -  chr3 (198295559 bp)
08:35:33.717 DEBUG GenomeLocParser -  chr9 (138394717 bp)
08:35:33.717 DEBUG GenomeLocParser -  chr10 (133797422 bp)
08:35:33.717 DEBUG GenomeLocParser -  chr13 (114364328 bp)
08:35:33.717 DEBUG GenomeLocParser -  chr15 (101991189 bp)
08:35:33.717 DEBUG GenomeLocParser -  chr17 (83257441 bp)
08:35:33.721 INFO  FeatureManager - Using codec BEDCodec to read file file:///home/dominm/SomaticPipeline/ref_files/bed_files/SSrep/SSrep_amplicons_v4.1.bed
08:35:33.729 DEBUG FeatureDataSource - Cache statistics for FeatureInput /home/dominm/SomaticPipeline/ref_files/bed_files/SSrep/SSrep_amplicons_v4.1.bed:/home/dominm/SomaticPipeline/ref_files/bed_files/SSrep/SSrep_amplicons_v4.1.bed:
08:35:33.729 DEBUG FeatureCache - Cache hit rate  was 0.00% (0 out of 0 total queries)
08:35:33.730 INFO  IntervalArgumentCollection - Processing 84444 bp from intervals
08:35:33.741 INFO  VariantAnnotator - Done initializing engine
08:35:33.742 INFO  VariantAnnotator - Shutting down engine
08:35:33.743 DEBUG FeatureDataSource - Cache statistics for FeatureInput drivingVariantFile:/mnt/scratch1/projects/SSrep/240605_M00321_0177_000000000-GLNFM-light/1109026765/240605_M00321_0177_000000000-GLNFM_1109026765.vcf:
08:35:33.743 DEBUG FeatureCache - Cache hit rate  was 0.00% (0 out of 0 total queries)
08:35:33.743 DEBUG FeatureDataSource - Cache statistics for FeatureInput drivingVariantFile:/mnt/scratch1/projects/SSrep/240605_M00321_0177_000000000-GLNFM-light/1109026765/240605_M00321_0177_000000000-GLNFM_1109026765.vcf:
08:35:33.743 DEBUG FeatureCache - Cache hit rate  was 0.00% (0 out of 0 total queries)
[July 23, 2024 at 8:35:33 AM GMT] org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=285212672
***********************************************************************

A USER ERROR has occurred: Reads sample '1109026765' from readgroups tags does not match any sample in the variant genotypes

***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
##contig=<ID=HLA-DRB1*15:01:01:03,length=11056>
##contig=<ID=HLA-DRB1*15:01:01:04,length=11056>
##contig=<ID=HLA-DRB1*15:02:01,length=10313>
##contig=<ID=HLA-DRB1*15:03:01:01,length=11567>
##contig=<ID=HLA-DRB1*15:03:01:02,length=11569>
##contig=<ID=HLA-DRB1*16:02:01,length=11005>
##fileDate=20240723
##reference=file:///mnt/data1/db/gcp-public-data--broad-references/hg38/v0/GIABv1mask/Homo_sapiens_assembly38.GIABv1mask.fasta
##source=Pisces 5.2.10.49
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  240605_M00321_0177_000000000-GLNFM_1109026765.bam
GATK4 • 236 views
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Entering edit mode
4 months ago

may be this is the problem

A USER ERROR has occurred: Reads sample '1109026765' from readgroups tags does not match any sample in the variant genotypes

your vcf contains a sample named '1109026765'

but the associated BAM file contains no Read group @RG with SM:1109026765
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