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Wrong annotation with Funcotator 1.7

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A. Brink

We started using GATK v4.1.9.0 Funcotator, using the latest (downloaded using FuncotatorDataSourceDownloader) v1.7.20200521s datasource.

However, when running the annotation on a hg19 mapped vcf file, the annotation of Gencode fields is terribly wrong. For example, completely wrong Gencode_34_variantClassification and Gencode_34_proteinChange fields.

Command used: 

Funcotator --variant input.vcf --reference $ref2 --ref-version hg19 -L $capture_targets -ip 100 --data-sources-path $DATA_SOURCES_DIR/funcotator_dataSources.v1.7.20200521s --output output.vcf --output-file-format VCF

When we use the previous v1.6.20190124s datasource, with the same command, annotation is correct and as expected.

For example:

hg19 chr17:7578492 C>T

Funcotator 1.7 output: MISSENSE c.686G>A p.C229Y

Funcotator 1.6 output: NONSENSE c.1043T>A p.L348*

 

What is going wrong here?

 

Funcotator 1.7
INFO: Failed to detect whether we are running on Google Compute Engine.
10:05:16.645 INFO  Funcotator - ------------------------------------------------------------
10:05:16.646 INFO  Funcotator - The Genome Analysis Toolkit (GATK) v4.1.9.0
10:05:16.646 INFO  Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/
10:05:16.646 INFO  Funcotator - Executing xxxx on Linux v3.10.0-693.17.1.el7.x86_64 amd64
10:05:16.646 INFO  Funcotator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_161-b14
10:05:16.646 INFO  Funcotator - Start Date/Time: December 18, 2020 10:05:16 AM CET
10:05:16.646 INFO  Funcotator - ------------------------------------------------------------
10:05:16.646 INFO  Funcotator - ------------------------------------------------------------
10:05:16.647 INFO  Funcotator - HTSJDK Version: 2.23.0
10:05:16.647 INFO  Funcotator - Picard Version: 2.23.3
10:05:16.647 INFO  Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
10:05:16.647 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:05:16.647 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:05:16.647 INFO  Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
10:05:16.647 INFO  Funcotator - Deflater: IntelDeflater
10:05:16.647 INFO  Funcotator - Inflater: IntelInflater
10:05:16.647 INFO  Funcotator - GCS max retries/reopens: 20
10:05:16.647 INFO  Funcotator - Requester pays: disabled
10:05:16.647 INFO  Funcotator - Initializing engine
10:05:17.145 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/vcf/mutect2/M3-0nM-MK-1_MuTect2_filtered.vcf
10:05:17.210 INFO  FeatureManager - Using codec BEDCodec to read file file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/Manifest/200527_HG19_KNOcustom3_capture_targets.bed
10:05:17.239 INFO  IntervalArgumentCollection - Processing 238722 bp from intervals
10:05:17.247 INFO  Funcotator - Done initializing engine
10:05:17.247 INFO  Funcotator - Validating sequence dictionaries...
10:05:17.248 INFO  Funcotator - Processing user transcripts/defaults/overrides...
10:05:17.249 INFO  Funcotator - Initializing data sources...
10:05:17.269 INFO  DataSourceUtils - Initializing data sources from directory: /home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s
10:05:17.280 INFO  DataSourceUtils - Data sources version: 1.7.2020429s
10:05:17.280 INFO  DataSourceUtils - Data sources source: ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/funcotator/funcotator_dataSources.v1.7.20200429s.tar.gz
10:05:17.280 INFO  DataSourceUtils - Data sources alternate source: gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.7.20200429s.tar.gz
10:05:17.316 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/achilles_lineage_results.import.txt -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/achilles/hg19/achilles_lineage_results.import.txt
10:05:17.337 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/cosmic_tissue.tsv -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/cosmic_tissue/hg19/cosmic_tissue.tsv
10:05:17.347 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/hgnc_download_Nov302017.tsv -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/hgnc/hg19/hgnc_download_Nov302017.tsv
10:05:17.382 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/clinvar_20180401.vcf -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/clinvar/hg19/clinvar_20180401.vcf
10:05:17.393 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/gencode_xrefseq_v75_37.tsv -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
10:05:17.408 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/clinvar_hgmd.tsv -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/clinvar_hgmd/hg19/clinvar_hgmd.tsv
10:05:18.615 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/gencode.v34lift37.annotation.REORDERED.gtf -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/gencode/hg19/gencode.v34lift37.annotation.REORDERED.gtf
10:05:18.615 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/gencode.v34lift37.pc_transcripts.fa -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/gencode/hg19/gencode.v34lift37.pc_transcripts.fa
10:05:18.632 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/Cosmic.db -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/cosmic/hg19/Cosmic.db
10:05:19.077 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/simple_uniprot_Dec012014.tsv -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
10:05:19.091 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/dnaRepairGenes.20180524T145835.csv -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/dna_repair_genes/hg19/dnaRepairGenes.20180524T145835.csv
10:05:19.099 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
10:05:19.136 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
10:05:19.148 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
10:05:19.162 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/oreganno.tsv -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/oreganno/hg19/oreganno.tsv
10:05:19.176 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/cosmic_fusion.tsv -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/cosmic_fusion/hg19/cosmic_fusion.tsv
10:05:19.189 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/hg19_All_20180423.vcf.gz -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/dbsnp/hg19/hg19_All_20180423.vcf.gz
10:05:19.189 INFO  Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)...
10:05:19.191 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/achilles_lineage_results.import.txt -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/achilles/hg19/achilles_lineage_results.import.txt
10:05:19.214 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/cosmic_tissue.tsv -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/cosmic_tissue/hg19/cosmic_tissue.tsv
10:05:19.288 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/hgnc_download_Nov302017.tsv -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/hgnc/hg19/hgnc_download_Nov302017.tsv
10:05:19.444 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/clinvar_20180401.vcf -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/clinvar/hg19/clinvar_20180401.vcf
10:05:19.444 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar_VCF : 100000
10:05:19.459 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/clinvar/hg19/clinvar_20180401.vcf
10:05:19.688 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/clinvar_20180401.vcf -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/clinvar/hg19/clinvar_20180401.vcf
10:05:19.782 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/clinvar/hg19/clinvar_20180401.vcf
10:05:19.883 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/gencode_xrefseq_v75_37.tsv -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv
10:05:20.015 INFO  DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000
10:05:20.021 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/clinvar_hgmd.tsv -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/clinvar_hgmd/hg19/clinvar_hgmd.tsv
10:05:20.028 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/clinvar_hgmd/hg19/clinvar_hgmd.config
10:05:20.164 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/clinvar_hgmd.tsv -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/clinvar_hgmd/hg19/clinvar_hgmd.tsv
10:05:20.164 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/clinvar_hgmd.tsv -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/clinvar_hgmd/hg19/clinvar_hgmd.tsv
WARNING 2020-12-18 10:05:20     AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
10:05:20.168 INFO  DataSourceUtils - Setting lookahead cache for data source: gnomAD_exome : 100000
10:05:23.181 INFO  FeatureManager - Using codec VCFCodec to read file gs://broad-public-datasets/funcotator/gnomAD_2.1_VCF_INFO_AF_Only/hg19/gnomad.exomes.r2.1.sites.INFO_ANNOTATIONS_FIXED.vcf.bgz
10:05:30.559 INFO  FeatureManager - Using codec VCFCodec to read file gs://broad-public-datasets/funcotator/gnomAD_2.1_VCF_INFO_AF_Only/hg19/gnomad.exomes.r2.1.sites.INFO_ANNOTATIONS_FIXED.vcf.bgz
10:05:31.510 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/gencode.v34lift37.annotation.REORDERED.gtf -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/gencode/hg19/gencode.v34lift37.annotation.REORDERED.gtf
10:05:31.510 INFO  DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000
10:05:31.525 INFO  FeatureManager - Using codec GencodeGtfCodec to read file file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/gencode/hg19/gencode.v34lift37.annotation.REORDERED.gtf
10:05:31.611 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/gencode.v34lift37.pc_transcripts.fa -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/gencode/hg19/gencode.v34lift37.pc_transcripts.fa
10:05:37.142 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/Cosmic.db -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/cosmic/hg19/Cosmic.db
10:05:38.046 INFO  DataSourceUtils - Setting lookahead cache for data source: gnomAD_genome : 100000
10:05:41.491 INFO  FeatureManager - Using codec VCFCodec to read file gs://broad-public-datasets/funcotator/gnomAD_2.1_VCF_INFO_AF_Only/hg19/gnomad.genomes.r2.1.sites.INFO_ANNOTATIONS_FIXED.vcf.bgz
10:05:51.224 INFO  FeatureManager - Using codec VCFCodec to read file gs://broad-public-datasets/funcotator/gnomAD_2.1_VCF_INFO_AF_Only/hg19/gnomad.genomes.r2.1.sites.INFO_ANNOTATIONS_FIXED.vcf.bgz
10:05:52.556 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/simple_uniprot_Dec012014.tsv -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv
10:05:52.683 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/dnaRepairGenes.20180524T145835.csv -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/dna_repair_genes/hg19/dnaRepairGenes.20180524T145835.csv
10:05:52.694 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt
10:05:52.711 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/Familial_Cancer_Genes.no_dupes.tsv -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv
10:05:52.720 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/gencode_xhgnc_v75_37.hg19.tsv -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv
10:05:53.755 INFO  DataSourceUtils - Setting lookahead cache for data source: Oreganno : 100000
10:05:53.757 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/oreganno.tsv -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/oreganno/hg19/oreganno.tsv
10:05:53.762 INFO  FeatureManager - Using codec XsvLocatableTableCodec to read file file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/oreganno/hg19/oreganno.config
10:05:53.847 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/oreganno.tsv -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/oreganno/hg19/oreganno.tsv
10:05:53.848 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/oreganno.tsv -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/oreganno/hg19/oreganno.tsv
WARNING 2020-12-18 10:05:53     AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream
10:05:53.849 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/cosmic_fusion.tsv -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/cosmic_fusion/hg19/cosmic_fusion.tsv
10:05:53.869 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/hg19_All_20180423.vcf.gz -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/dbsnp/hg19/hg19_All_20180423.vcf.gz
10:05:53.869 INFO  DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000
10:05:53.881 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/dbsnp/hg19/hg19_All_20180423.vcf.gz
10:05:54.015 INFO  DataSourceUtils - Resolved data source file path: file:///home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/hg19_All_20180423.vcf.gz -> file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/dbsnp/hg19/hg19_All_20180423.vcf.gz
10:05:54.064 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/Test/Pipelines/SeqCap_Pipeline/Necessary_files/GATK/funcotator_dataSources.v1.7.20200521s/dbsnp/hg19/hg19_All_20180423.vcf.gz
10:05:54.110 INFO  Funcotator - Initializing Funcotator Engine...
10:05:54.138 INFO  FuncotatorEngine - Using given VCF and Reference.  No conversion required.
10:05:54.138 INFO  Funcotator - Creating a VCF file for output: file:/home/Test/Pipelines/SeqCap_Pipeline/Test/Annotation/funcotator/mutect2/M3-0nM-MK-1_MuTect2_funcotatorS_1.vcf
10:05:54.189 INFO  ProgressMeter - Starting traversal
10:05:54.189 INFO  ProgressMeter -        Current Locus  Elapsed Minutes    Variants Processed  Variants/Minute
10:09:20.968 INFO  ProgressMeter -             unmapped              3.4                   507            147.1
10:09:20.969 INFO  ProgressMeter - Traversal complete. Processed 507 total variants in 3.4 minutes.
10:09:20.969 INFO  VcfFuncotationFactory - ClinVar_VCF 20180401 cache hits/total: 0/87
10:09:20.969 INFO  VcfFuncotationFactory - dbSNP 9606_b151 cache hits/total: 0/491
10:09:20.969 INFO  VcfFuncotationFactory - gnomAD_exome 2.1 cache hits/total: 0/318
10:09:20.969 INFO  VcfFuncotationFactory - gnomAD_genome 2.1 cache hits/total: 0/455
10:09:21.088 INFO  Funcotator - Shutting down engine
[December 18, 2020 10:09:23 AM CET] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 4.11 minutes.
Runtime.totalMemory()=5446828032
Tool returned:
TRUE
0

3 comments

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    A. Brink

    I've done some additional tests.

    - Also when using the v1.7.20200521g germline datasource the annotation mistakes are there.

    - Also when I run the Funcotator command without the -L and -ip options the annotation screwup is there.

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    A. Brink

    And more tests:

    - When first lifting my vcf file from hg19 to hg38 using GATK LiftoverVcf, and then running Funcotator using the v1.7.20200521g germline datasource with --ref-version hg38 results in output that is correct, and comparable to the v1.6 with --ref-version hg19.

    - The annotation output seems wrong for certain genes in my capture panel, some genes turn out to be fine.

    - For example, variants in HLA-A (chr6) and RB1 (chr13) are correctly annotated with  v1.6.20190124g hg19, v1.7.20200521g hg19 and v1.7.20200521g hg38. In contrast, variants in NOTCH1 (chr9) and TP53 (chr17) are correctly annotated with v1.6.20190124g hg19 and v1.7.20200521g hg38, but wrongly annotated when using v1.7.20200521g hg19.

     
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    Genevieve Brandt (she/her)

    Hi A. Brink, were you able to solve this issue? Your question was posted while our GATK Team was Out of Office and we did not get to your question.

    If you still would like support from the GATK Team, please repost your question with [Repost] in the title and we will get to it as soon as possible.

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