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Official code repository for GATK versions 4 and up
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no annotation warning with Funcotator #7158

Open sheucke opened 3 years ago

sheucke commented 3 years ago

vcf file:

fileformat=VCFv4.2

FORMAT=

FORMAT=

FORMAT=

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TUMOR NORMAL

2 220439700 . G GCT . . . GT:AD:DP 0/1:21,72:93 0/0:51,0:51 3 52437426 . GCCCACCTGTCAGCGCCAGGGGA G . . . GT:AD:DP 0/1:10,10:20 0/0:11,0:11 3 52437701 . GTGGGTGA G . . . GT:AD:DP 0/1:10,10:20 0/0:11,0:11 3 52443788 . ATGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC A . . . GT:AD:DP 0/1:10,10:20 0/0:11,0:11 3 178928219 . G GATA . . . GT:AD:DP 0/1:21,22:43 0/0:11,0:11 3 178936091 . G A . . . GT:AD:DP 0/1:21,22:43 0/0:11,0:11 5 1295228 . G A . . . GT:AD:DP 0/1:10,10:20 0/0:11,0:11 5 1295250 . G A . . . GT:AD:DP 0/1:10,10:20 0/0:11,0:11 5 56177848 . TCAA T . . . GT:AD:DP 0/1:34,16:50 0/0:46,0:46 5 112174757 . GAAGA G,GGA . . . GT:AD:DP 0/2:12,0,8:20 0/0:30,0,2:32 5 112174757 . GAAGA G,GCA . . . GT:AD:DP 1/2:0,12,8:20 1/1:0,30,2:32 5 112174757 . GAAGA G,GGA . . . GT:AD:DP 0/1:12,8,0:20 0/2:30,0,2:32 5 112174757 . GAAGA G,GGA . . . GT:AD:DP 0/2:12,0,8:20 0/1:30,2,0:32 6 41903782 . AG CA . . . GT:AD:DP 0/1:28,22:50 0/0:48,0:48 7 116412043 . G C . . . GT:AD:DP 0/1:25,22:47 0/0:98,1:99 13 28608242 . A AACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG . . . GT:AD:DP 0/1:10,10:20 0/0:11,0:11 17 7579312 . C A . . . GT:AD:DP 0/1:20,22:42 0/0:18,1:1

funcotator output:

(gatk) root@75181703d894:/gatk# ./gatk Funcotator \

 --variant ./my_data/test_b37.vcf \
 --reference ./my_data/human_g1k_v37.fasta \
 --ref-version hg19 \
 --data-sources-path ./my_data/funcotator_dataSources.v1.7.20200521s \
 --output ./my_data/variants.funcotated.maf \
 --output-file-format MAF \
 --disable-sequence-dictionary-validation

Using GATK jar /gatk/gatk-package-4.2.0.0-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-4.2.0.0-local.jar Funcotator --variant ./my_data/test_b37.vcf --reference ./my_data/human_g1k_v37.fasta --ref-version hg19 --data-sources-path ./my_data/funcotator_dataSources.v1.7.20200521s --output ./my_data/variants.funcotated.maf --output-file-format MAF --disable-sequence-dictionary-validation 12:11:19.732 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.2.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so Mar 24, 2021 12:11:19 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine INFO: Failed to detect whether we are running on Google Compute Engine. 12:11:19.904 INFO Funcotator - ------------------------------------------------------------ 12:11:19.904 INFO Funcotator - The Genome Analysis Toolkit (GATK) v4.2.0.0 12:11:19.904 INFO Funcotator - For support and documentation go to https://software.broadinstitute.org/gatk/ 12:11:19.905 INFO Funcotator - Executing as root@75181703d894 on Linux v4.15.0-132-generic amd64 12:11:19.905 INFO Funcotator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-8u242-b08-0ubuntu3~18.04-b08 12:11:19.905 INFO Funcotator - Start Date/Time: March 24, 2021 12:11:19 PM GMT 12:11:19.905 INFO Funcotator - ------------------------------------------------------------ 12:11:19.905 INFO Funcotator - ------------------------------------------------------------ 12:11:19.906 INFO Funcotator - HTSJDK Version: 2.24.0 12:11:19.906 INFO Funcotator - Picard Version: 2.25.0 12:11:19.906 INFO Funcotator - Built for Spark Version: 2.4.5 12:11:19.906 INFO Funcotator - HTSJDK Defaults.COMPRESSION_LEVEL : 2 12:11:19.906 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 12:11:19.906 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 12:11:19.907 INFO Funcotator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 12:11:19.907 INFO Funcotator - Deflater: IntelDeflater 12:11:19.907 INFO Funcotator - Inflater: IntelInflater 12:11:19.907 INFO Funcotator - GCS max retries/reopens: 20 12:11:19.907 INFO Funcotator - Requester pays: disabled 12:11:19.907 INFO Funcotator - Initializing engine 12:11:20.348 INFO FeatureManager - Using codec VCFCodec to read file file:///gatk/./my_data/test_b37.vcf 12:11:20.368 INFO Funcotator - Done initializing engine 12:11:20.368 INFO Funcotator - Skipping sequence dictionary validation. 12:11:20.369 INFO Funcotator - Processing user transcripts/defaults/overrides... 12:11:20.370 INFO Funcotator - Initializing data sources... 12:11:20.375 INFO DataSourceUtils - Initializing data sources from directory: ./my_data/funcotator_dataSources.v1.7.20200521s 12:11:20.376 INFO DataSourceUtils - Data sources version: 1.7.2020429s 12:11:20.376 INFO DataSourceUtils - Data sources source: ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/funcotator/funcotator_dataSources.v1.7.20200429s.tar.gz 12:11:20.377 INFO DataSourceUtils - Data sources alternate source: gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.7.20200429s.tar.gz 12:11:20.388 INFO DataSourceUtils - Resolved data source file path: file:///gatk/gencode.v34lift37.annotation.REORDERED.gtf -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/gencode/hg19/gencode.v34lift37.annotation.REORDERED.gtf 12:11:20.389 INFO DataSourceUtils - Resolved data source file path: file:///gatk/gencode.v34lift37.pc_transcripts.fa -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/gencode/hg19/gencode.v34lift37.pc_transcripts.fa 12:11:20.391 INFO DataSourceUtils - Resolved data source file path: file:///gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv 12:11:20.393 INFO DataSourceUtils - Resolved data source file path: file:///gatk/gencode_xrefseq_v75_37.tsv -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv 12:11:20.396 INFO DataSourceUtils - Resolved data source file path: file:///gatk/hgnc_download_Nov302017.tsv -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/hgnc/hg19/hgnc_download_Nov302017.tsv 12:11:20.397 INFO DataSourceUtils - Resolved data source file path: file:///gatk/hg19_All_20180423.vcf.gz -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/dbsnp/hg19/hg19_All_20180423.vcf.gz 12:11:20.400 INFO DataSourceUtils - Resolved data source file path: file:///gatk/oreganno.tsv -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/oreganno/hg19/oreganno.tsv 12:11:20.402 INFO DataSourceUtils - Resolved data source file path: file:///gatk/cosmic_tissue.tsv -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/cosmic_tissue/hg19/cosmic_tissue.tsv 12:11:20.404 INFO DataSourceUtils - Resolved data source file path: file:///gatk/cosmic_fusion.tsv -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/cosmic_fusion/hg19/cosmic_fusion.tsv 12:11:20.406 INFO DataSourceUtils - Resolved data source file path: file:///gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv 12:11:20.408 INFO DataSourceUtils - Resolved data source file path: file:///gatk/Cosmic.db -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/cosmic/hg19/Cosmic.db 12:11:20.409 INFO DataSourceUtils - Resolved data source file path: file:///gatk/clinvar_hgmd.tsv -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/clinvar_hgmd/hg19/clinvar_hgmd.tsv 12:11:20.411 INFO DataSourceUtils - Resolved data source file path: file:///gatk/dnaRepairGenes.20180524T145835.csv -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/dna_repair_genes/hg19/dnaRepairGenes.20180524T145835.csv 12:11:20.413 INFO DataSourceUtils - Resolved data source file path: file:///gatk/simple_uniprot_Dec012014.tsv -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv 12:11:20.415 INFO DataSourceUtils - Resolved data source file path: file:///gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt 12:11:20.417 INFO DataSourceUtils - Resolved data source file path: file:///gatk/clinvar_20180401.vcf -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/clinvar/hg19/clinvar_20180401.vcf 12:11:20.418 INFO DataSourceUtils - Resolved data source file path: file:///gatk/achilles_lineage_results.import.txt -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/achilles/hg19/achilles_lineage_results.import.txt 12:11:20.419 INFO Funcotator - Finalizing data sources (this step can be long if data sources are cloud-based)... 12:11:20.420 INFO DataSourceUtils - Resolved data source file path: file:///gatk/gencode.v34lift37.annotation.REORDERED.gtf -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/gencode/hg19/gencode.v34lift37.annotation.REORDERED.gtf 12:11:20.420 INFO DataSourceUtils - Setting lookahead cache for data source: Gencode : 100000 12:11:20.452 INFO FeatureManager - Using codec GencodeGtfCodec to read file file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/gencode/hg19/gencode.v34lift37.annotation.REORDERED.gtf 12:11:20.517 INFO DataSourceUtils - Resolved data source file path: file:///gatk/gencode.v34lift37.pc_transcripts.fa -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/gencode/hg19/gencode.v34lift37.pc_transcripts.fa 12:11:27.980 INFO DataSourceUtils - Resolved data source file path: file:///gatk/Familial_Cancer_Genes.no_dupes.tsv -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/familial/hg19/Familial_Cancer_Genes.no_dupes.tsv 12:11:27.985 INFO DataSourceUtils - Resolved data source file path: file:///gatk/gencode_xrefseq_v75_37.tsv -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/gencode_xrefseq/hg19/gencode_xrefseq_v75_37.tsv 12:11:28.126 INFO DataSourceUtils - Resolved data source file path: file:///gatk/hgnc_download_Nov302017.tsv -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/hgnc/hg19/hgnc_download_Nov302017.tsv 12:11:28.270 INFO DataSourceUtils - Resolved data source file path: file:///gatk/hg19_All_20180423.vcf.gz -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/dbsnp/hg19/hg19_All_20180423.vcf.gz 12:11:28.270 INFO DataSourceUtils - Setting lookahead cache for data source: dbSNP : 100000 12:11:28.277 INFO FeatureManager - Using codec VCFCodec to read file file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/dbsnp/hg19/hg19_All_20180423.vcf.gz 12:11:28.426 INFO DataSourceUtils - Resolved data source file path: file:///gatk/hg19_All_20180423.vcf.gz -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/dbsnp/hg19/hg19_All_20180423.vcf.gz 12:11:28.771 INFO FeatureManager - Using codec VCFCodec to read file file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/dbsnp/hg19/hg19_All_20180423.vcf.gz 12:11:28.877 INFO DataSourceUtils - Setting lookahead cache for data source: Oreganno : 100000 12:11:28.882 INFO DataSourceUtils - Resolved data source file path: file:///gatk/oreganno.tsv -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/oreganno/hg19/oreganno.tsv 12:11:28.883 INFO FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/oreganno/hg19/oreganno.config 12:11:28.905 INFO DataSourceUtils - Resolved data source file path: file:///gatk/oreganno.tsv -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/oreganno/hg19/oreganno.tsv 12:11:28.906 INFO DataSourceUtils - Resolved data source file path: file:///gatk/oreganno.tsv -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/oreganno/hg19/oreganno.tsv WARNING 2021-03-24 12:11:28 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream 12:11:28.910 INFO DataSourceUtils - Resolved data source file path: file:///gatk/cosmic_tissue.tsv -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/cosmic_tissue/hg19/cosmic_tissue.tsv 12:11:28.930 INFO DataSourceUtils - Resolved data source file path: file:///gatk/cosmic_fusion.tsv -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/cosmic_fusion/hg19/cosmic_fusion.tsv 12:11:28.932 INFO DataSourceUtils - Resolved data source file path: file:///gatk/gencode_xhgnc_v75_37.hg19.tsv -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/gencode_xhgnc/hg19/gencode_xhgnc_v75_37.hg19.tsv 12:11:29.933 INFO DataSourceUtils - Resolved data source file path: file:///gatk/Cosmic.db -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/cosmic/hg19/Cosmic.db 12:11:30.002 INFO DataSourceUtils - Setting lookahead cache for data source: ClinVar : 100000 12:11:30.004 INFO DataSourceUtils - Resolved data source file path: file:///gatk/clinvar_hgmd.tsv -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/clinvar_hgmd/hg19/clinvar_hgmd.tsv 12:11:30.005 INFO FeatureManager - Using codec XsvLocatableTableCodec to read file file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/clinvar_hgmd/hg19/clinvar_hgmd.config 12:11:30.052 INFO DataSourceUtils - Resolved data source file path: file:///gatk/clinvar_hgmd.tsv -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/clinvar_hgmd/hg19/clinvar_hgmd.tsv 12:11:30.053 INFO DataSourceUtils - Resolved data source file path: file:///gatk/clinvar_hgmd.tsv -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/clinvar_hgmd/hg19/clinvar_hgmd.tsv WARNING 2021-03-24 12:11:30 AsciiLineReader Creating an indexable source for an AsciiFeatureCodec using a stream that is neither a PositionalBufferedStream nor a BlockCompressedInputStream 12:11:30.054 INFO DataSourceUtils - Resolved data source file path: file:///gatk/dnaRepairGenes.20180524T145835.csv -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/dna_repair_genes/hg19/dnaRepairGenes.20180524T145835.csv 12:11:30.055 INFO DataSourceUtils - Resolved data source file path: file:///gatk/simple_uniprot_Dec012014.tsv -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/simple_uniprot/hg19/simple_uniprot_Dec012014.tsv 12:11:30.101 INFO DataSourceUtils - Resolved data source file path: file:///gatk/CancerGeneCensus_Table_1_full_2012-03-15.txt -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/cancer_gene_census/hg19/CancerGeneCensus_Table_1_full_2012-03-15.txt 12:11:30.104 INFO DataSourceUtils - Resolved data source file path: file:///gatk/clinvar_20180401.vcf -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/clinvar/hg19/clinvar_20180401.vcf 12:11:30.104 INFO DataSourceUtils - Setting lookahead cache for data source: ClinVar_VCF : 100000 12:11:30.106 INFO FeatureManager - Using codec VCFCodec to read file file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/clinvar/hg19/clinvar_20180401.vcf 12:11:30.163 INFO DataSourceUtils - Resolved data source file path: file:///gatk/clinvar_20180401.vcf -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/clinvar/hg19/clinvar_20180401.vcf 12:11:32.523 INFO FeatureManager - Using codec VCFCodec to read file file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/clinvar/hg19/clinvar_20180401.vcf 12:11:32.592 INFO DataSourceUtils - Resolved data source file path: file:///gatk/achilles_lineage_results.import.txt -> file:///gatk/./my_data/funcotator_dataSources.v1.7.20200521s/achilles/hg19/achilles_lineage_results.import.txt 12:11:32.594 INFO Funcotator - Initializing Funcotator Engine... 12:11:32.595 INFO FuncotatorEngine - Using given VCF and Reference. No conversion required. 12:11:32.595 INFO Funcotator - Creating a MAF file for output: file:/gatk/./mydata/variants.funcotated.maf 12:11:32.616 INFO ProgressMeter - Starting traversal 12:11:32.616 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 12:11:32.827 INFO ProgressMeter - unmapped 0.0 17 4857.1 12:11:32.827 INFO ProgressMeter - Traversal complete. Processed 17 total variants in 0.0 minutes. 12:11:32.827 WARN Funcotator - ================================================================================ 12:11:32.827 WARN Funcotator -
12:11:32.827 WARN Funcotator - | || || | \ \ / / _ _ () | || || |
12:11:32.828 WARN Funcotator - | || || | \ \ /\ / / ` | '| ' | | ' \ / ` | | || || |
12:11:32.828 WARN Funcotator - |||||| \ \V V / (| | | | | | | | | | | (| | ||||||
12:11:32.828 WARN Funcotator - ()()() _/_/ _,|| || |||| ||\, | ()()(_)
12:11:32.828 WARN Funcotator - |___/
12:11:32.828 WARN Funcotator - -------------------------------------------------------------------------------- 12:11:32.828 WARN Funcotator - Only IGRs were produced for this dataset. This STRONGLY indicates that this
12:11:32.828 WARN Funcotator - run was misconfigured.
12:11:32.828 WARN Funcotator - You MUST check your data sources to make sure they are correct for these data. 12:11:32.828 WARN Funcotator - ================================================================================ 12:11:32.829 INFO VcfFuncotationFactory - ClinVar_VCF 20180401 cache hits/total: 0/0 12:11:32.829 INFO VcfFuncotationFactory - dbSNP 9606_b151 cache hits/total: 0/0 12:11:32.830 INFO Funcotator - Shutting down engine [March 24, 2021 12:11:32 PM GMT] org.broadinstitute.hellbender.tools.funcotator.Funcotator done. Elapsed time: 0.22 minutes. Runtime.totalMemory()=1793064960 Tool returned: true (gatk) root@75181703d894:/gatk#

the variants.funcotated.maf:

version 2.4

fileformat=VCFv4.2

FORMAT=

FORMAT=

FORMAT=

source=Funcotator

GATKCommandLine=<ID=Funcotator,CommandLine="Funcotator --output ./my_data/variants.funcotated.maf --ref-version hg19 --data-sources-path ./my_data/funcotator_dataSources.v1.7.20200521s --output-file-format MAF --variant ./my_data/test_b37.vcf --reference ./my_data/human_g1k_v37.fasta --disable-sequence-dictionary-validation true --remove-filtered-variants false --five-prime-flank-size 5000 --three-prime-flank-size 0 --force-b37-to-hg19-reference-contig-conversion false --transcript-selection-mode CANONICAL --lookahead-cache-bp 100000 --min-num-bases-for-segment-funcotation 150 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version="4.2.0.0",Date="March 24, 2021 12:11:32 PM GMT">

Funcotator 4.2.0.0 | Date 20211124T121132 | Gencode 34 CANONICAL | Achilles 110303 | CGC full_2012_03-15 | ClinVar 12.03.20 | ClinVar_VCF 20180401 | Cosmic v84 | CosmicFusion v84 | CosmicTissue v83 | DNARepairGenes 20180524T145835 | Familial_Cancer_Genes 20110905 | Gencode_XHGNC 75_37 | Gencode_XRefSeq 75_37 | HGNC Nov302017 | Oreganno 20160119 | Simple_Uniprot 2014_12 | dbSNP 9606_b151

Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID Genome_Change Annotation_Transcript Transcript_Strand Transcript_Exon Transcript_Position cDNA_Change Codon_Change Protein_Change Other_Transcripts Refseq_mRNA_Id Refseq_prot_Id SwissProt_acc_Id SwissProt_entry_Id Description UniProt_AApos UniProt_Region UniProt_Site UniProt_Natural_Variations UniProt_Experimental_Info GO_Biological_Process GO_Cellular_Component GO_Molecular_Function COSMIC_overlapping_mutations COSMIC_fusion_genes COSMIC_tissue_types_affected COSMIC_total_alterations_in_gene Tumorscape_Amplification_Peaks Tumorscape_Deletion_Peaks TCGAscape_Amplification_Peaks TCGAscape_Deletion_Peaks DrugBank ref_context gc_content CCLE_ONCOMAP_overlapping_mutations CCLE_ONCOMAP_total_mutations_in_gene CGC_Mutation_Type CGC_Translocation_Partner CGC_Tumor_Types_Somatic CGC_Tumor_Types_Germline CGC_Other_Diseases DNARepairGenes_Activity_linked_to_OMIM FamilialCancerDatabase_Syndromes MUTSIG_Published_Results OREGANNO_ID OREGANNO_Values tumor_f t_alt_count t_ref_count n_alt_count n_ref_count Gencode_34_secondaryVariantClassification Achilles_Top_Genes CGC_Name CGC_GeneID CGC_Chr CGC_Chr_Band CGC_Cancer_Somatic_Mut CGC_Cancer_Germline_Mut CGC_Cancer_Syndrome CGC_Tissue_Type CGC_Cancer_Molecular_Genetics CGC_Other_Germline_Mut ClinVar_HGMD_ID ClinVar_SYM ClinVar_TYPE ClinVar_ASSEMBLY ClinVar_rs ClinVar_VCF_AF_ESP ClinVar_VCF_AF_EXAC ClinVar_VCF_AF_TGP ClinVar_VCF_ALLELEID ClinVar_VCF_CLNDISDB ClinVar_VCF_CLNDISDBINCL ClinVar_VCF_CLNDN ClinVar_VCF_CLNDNINCL ClinVar_VCF_CLNHGVS ClinVar_VCF_CLNREVSTAT ClinVar_VCF_CLNSIG ClinVar_VCF_CLNSIGCONF ClinVar_VCF_CLNSIGINCL ClinVar_VCF_CLNVC ClinVar_VCF_CLNVCSO ClinVar_VCF_CLNVI ClinVar_VCF_DBVARID ClinVar_VCF_GENEINFO ClinVar_VCF_MC ClinVar_VCF_ORIGIN ClinVar_VCF_RS ClinVar_VCF_SSR ClinVar_VCF_ID ClinVar_VCF_FILTER CosmicFusion_fusion_id DNARepairGenes_Chromosome_location_linked_to_NCBI_MapView DNARepairGenes_Accession_number_linked_to_NCBI_Entrez Familial_Cancer_Genes_Synonym Familial_Cancer_Genes_Reference Gencode_XHGNC_hgnc_id HGNC_HGNC_ID HGNC_Status HGNC_Locus_Type HGNC_Locus_Group HGNC_Previous_Symbols HGNC_Previous_Name HGNC_Synonyms HGNC_Name_Synonyms HGNC_Chromosome HGNC_Date_Modified HGNC_Date_Symbol_Changed HGNC_Date_Name_Changed HGNC_Accession_Numbers HGNC_Enzyme_IDs HGNC_Ensembl_Gene_ID HGNC_Pubmed_IDs HGNC_RefSeq_IDs HGNC_Gene_Family_ID HGNC_Gene_Family_Name HGNC_CCDS_IDs HGNC_Vega_ID HGNC_OMIM_ID(supplied_by_OMIM) HGNC_RefSeq(supplied_by_NCBI) HGNC_UniProt_ID(supplied_by_UniProt) HGNC_Ensembl_ID(supplied_by_Ensembl) HGNC_UCSC_ID(supplied_by_UCSC) Oreganno_Build Simple_Uniprot_alt_uniprot_accessions dbSNP_ASP dbSNP_ASS dbSNP_CAF dbSNP_CDA dbSNP_CFL dbSNP_COMMON dbSNP_DSS dbSNP_G5 dbSNP_G5A dbSNP_GENEINFO dbSNP_GNO dbSNP_HD dbSNP_INT dbSNP_KGPhase1 dbSNP_KGPhase3 dbSNP_LSD dbSNP_MTP dbSNP_MUT dbSNP_NOC dbSNP_NOV dbSNP_NSF dbSNP_NSM dbSNP_NSN dbSNP_OM dbSNP_OTH dbSNP_PM dbSNP_PMC dbSNP_R3 dbSNP_R5 dbSNP_REF dbSNP_RV dbSNP_S3D dbSNP_SAO dbSNP_SLO dbSNP_SSR dbSNP_SYN dbSNP_TOPMED dbSNP_TPA dbSNP_U3 dbSNP_U5 dbSNP_VC dbSNP_VP dbSNP_WGT dbSNP_WTD dbSNP_dbSNPBuildID dbSNP_ID dbSNP_FILTER HGNC_Entrez_Gene_ID(supplied_by_NCBI) dbSNP_RSPOS dbSNP_VLD Unknown UNKNOWN hg19 2 220439700 220439701 + IGR INS - - CT UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN NA NA UNKNOWN UNKNOWN UNKNOWN g.2:220439700_220439701insCT no_transcript UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN GCCACCTCTGCTCTCTCTCT 0.67 UNKNOWN UNKNOWN UNKNOWN 72 21 0 51 false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false Unknown UNKNOWN hg19 3 52437427 52437448 + IGR DEL CCCACCTGTCAGCGCCAGGGGA CCCACCTGTCAGCGCCAGGGGA - UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN NA NA UNKNOWN UNKNOWN UNKNOWN g.3:52437427_52437448delCCCACCTGTCAGCGCCAGGGGA no_transcript UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN CAGTCCAAGGCCCACCTGTCAGCGCCAGGGGACTCAGCACCC 0.6137440758293838 UNKNOWN UNKNOWN UNKNOWN 10 10 0 11 false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false Unknown UNKNOWN hg19 3 52437702 52437708 + IGR DEL TGGGTGA TGGGTGA - UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN NA NA UNKNOWN UNKNOWN UNKNOWN g.3:52437702_52437708delTGGGTGA no_transcript UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN TTGCTGGGGGTGGGTGAGGGCTGCGAG 0.5921375921375921 UNKNOWN UNKNOWN UNKNOWN 10 10 0 11 false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false Unknown UNKNOWN hg19 3 52443789 52443850 + IGR DEL TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC TGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC - UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN NA NA UNKNOWN UNKNOWN UNKNOWN g.3:52443789_52443850delTGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCC no_transcript UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN GAGGGGGTGATGGTCAGGCAGGCGCGTCCCGGGCCCATCCGGCCTCCCCAGCCCCTGGCCCTCCCGGTCCCCTCCTCACCTG 0.6991341991341992 UNKNOWN UNKNOWN UNKNOWN 10 10 0 11 false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false Unknown UNKNOWN hg19 3 178928219 178928220 + IGR INS - - ATA UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN NA NA UNKNOWN UNKNOWN UNKNOWN g.3:178928219_178928220insATA no_transcript UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN ATCTCTTAGGAAACTCCATG 0.3725 UNKNOWN UNKNOWN UNKNOWN 22 21 0 11 false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false Unknown UNKNOWN hg19 3 178936091 178936091 + IGR SNP G G A UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN NA NA UNKNOWN UNKNOWN UNKNOWN g.3:178936091G>A no_transcript UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN TGAAATCACTGAGCAGGAGAA 0.29925187032418954 UNKNOWN UNKNOWN UNKNOWN 22 21 0 11 false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false Unknown UNKNOWN hg19 5 1295228 1295228 + IGR SNP G G A UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN NA NA UNKNOWN UNKNOWN UNKNOWN g.5:1295228G>A no_transcript UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN AGGGCCCGGAGGGGGCTGGGC 0.7755610972568578 UNKNOWN UNKNOWN UNKNOWN 10 10 0 11 false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false Unknown UNKNOWN hg19 5 1295250 1295250 + IGR SNP G G A UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN NA NA UNKNOWN UNKNOWN UNKNOWN g.5:1295250G>A no_transcript UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN GGGGACCCGGGAGGGGTCGGG 0.7780548628428927 UNKNOWN UNKNOWN UNKNOWN 10 10 0 11 false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false Unknown UNKNOWN hg19 5 56177849 56177851 + IGR DEL CAA CAA - UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN NA NA UNKNOWN UNKNOWN UNKNOWN g.5:56177849_56177851delCAA no_transcript UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN CCTTCTAGTTCAACAACAACAAC 0.4491315136476427 UNKNOWN UNKNOWN UNKNOWN 16 34 0 46 false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false Unknown UNKNOWN hg19 5 112174758 112174761 + IGR DEL AAGA AAGA - UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN NA NA UNKNOWN UNKNOWN UNKNOWN g.5:112174758_112174761delAAGA no_transcript UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN CATGAAGAAGAAGAGAGACCAACA 0.37623762376237624 UNKNOWN UNKNOWN UNKNOWN 0 12 0 30 false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false Unknown UNKNOWN hg19 5 112174758 112174761 + IGR DEL GA GA - UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN NA NA UNKNOWN UNKNOWN UNKNOWN g.5:112174758_112174761delGA no_transcript UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN CATGAAGAAGAAGAGAGACCAACA 0.37623762376237624 UNKNOWN UNKNOWN UNKNOWN 8 12 2 30 false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false Unknown UNKNOWN hg19 5 112174758 112174761 + IGR DEL AAGA AAGA - UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN NA NA UNKNOWN UNKNOWN UNKNOWN g.5:112174758_112174761delAAGA no_transcript UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN CATGAAGAAGAAGAGAGACCAACA 0.37623762376237624 UNKNOWN UNKNOWN UNKNOWN 12 0 30 0 false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false Unknown UNKNOWN hg19 5 112174758 112174761 + IGR DEL GA GA - UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN NA NA UNKNOWN UNKNOWN UNKNOWN g.5:112174758_112174761delCA no_transcript UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN CATGAAGAAGAAGAGAGACCAACA 0.37623762376237624 UNKNOWN UNKNOWN UNKNOWN 8 0 2 0 false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false Unknown UNKNOWN hg19 5 112174758 112174761 + IGR DEL AAGA AAGA - UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN NA NA UNKNOWN UNKNOWN UNKNOWN g.5:112174758_112174761delAAGA no_transcript UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN CATGAAGAAGAAGAGAGACCAACA 0.37623762376237624 UNKNOWN UNKNOWN UNKNOWN 8 12 0 30 false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false Unknown UNKNOWN hg19 5 112174758 112174761 + IGR DEL GA GA - UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN NA NA UNKNOWN UNKNOWN UNKNOWN g.5:112174758_112174761delGA no_transcript UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN CATGAAGAAGAAGAGAGACCAACA 0.37623762376237624 UNKNOWN UNKNOWN UNKNOWN 0 12 2 30 false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false Unknown UNKNOWN hg19 5 112174758 112174761 + IGR DEL AAGA AAGA - UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN NA NA UNKNOWN UNKNOWN UNKNOWN g.5:112174758_112174761delAAGA no_transcript UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN CATGAAGAAGAAGAGAGACCAACA 0.37623762376237624 UNKNOWN UNKNOWN UNKNOWN 0 12 2 30 false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false Unknown UNKNOWN hg19 5 112174758 112174761 + IGR DEL GA GA - UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN NA NA UNKNOWN UNKNOWN UNKNOWN g.5:112174758_112174761delGA no_transcript UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN CATGAAGAAGAAGAGAGACCAACA 0.37623762376237624 UNKNOWN UNKNOWN UNKNOWN 8 12 0 30 false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false Unknown UNKNOWN hg19 6 41903782 41903783 + IGR DNP AG AG CA UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN NA NA UNKNOWN UNKNOWN UNKNOWN g.6:41903782_41903783AG>CA no_transcript UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN CTGGTCTGAGAGGCTTCCCTGA 0.6318407960199005 UNKNOWN UNKNOWN UNKNOWN 22 28 0 48 false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false Unknown UNKNOWN hg19 7 116412043 116412043 + IGR SNP G G C UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN NA NA UNKNOWN UNKNOWN UNKNOWN g.7:116412043G>C no_transcript UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN TTTTCCAGAAGGTATATTTCA 0.3566084788029925 UNKNOWN UNKNOWN UNKNOWN 22 25 1 98 false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false Unknown UNKNOWN hg19 13 28608242 28608243 + IGR INS - - ACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN NA NA UNKNOWN UNKNOWN UNKNOWN g.13:28608242_28608243insACTCCCATTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTACCCCCTCGGGGGG no_transcript UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN TCTCTTGGAAACTCCCATTT 0.38 UNKNOWN UNKNOWN UNKNOWN 10 10 0 11 false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false Unknown UNKNOWN hg19 17 7579312 7579312 + IGR SNP C C A UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN NA NA UNKNOWN UNKNOWN UNKNOWN g.17:7579312C>A no_transcript UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN UNKNOWN GGCAACTGACCGTGCAAGTCA 0.5461346633416458 UNKNOWN UNKNOWN UNKNOWN 22 20 1 18 false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false false

jonn-smith commented 3 years ago

@sheucke Based on your VCF filename it looks like it was created with the b37 reference. Try re-running Funcotator with the b37 reference or the hg19 reference. The reference you're using with this call to Funcotator (human_g1k_v37.fasta) is slightly different than b37 (it doesn't contain the NC_007605 contig - the Epstein-Barr virus) and has larger differences when compared to hg19 (contig names are different, different sequence information).

Here is a comparison of the "hg19" references: https://gatk.broadinstitute.org/hc/en-us/articles/360035890711