GATK Funcotator Variant_Classification

Question

[haiying.kong]

If you are seeing an error, please provide(REQUIRED) : a) GATK version used: b) Exact command used: c) Entire error log:

If not an error, choose a category for your question(REQUIRED): a)How do I (......)? b) What does (......) mean? c) Why do I see (......)? d) Where do I find (......)? e) Will (......) be in future releases?

gatk Funcotator \
-R $hg -V ${Lock_VarDict_dir}/$sample.vcf -O ${Result_VarDict_dir}/$sample.maf \
--output-file-format MAF --ref-version hg38 --data-sources-path $Funcotator_DB \
--disable-sequence-dictionary-validation

c) Entire error log: There is no error. Everything worked out, but in the output something is wrong.

Funcotator classified one very canonical missense mutation in acute myeloid leukemia as intron. Please help me.

The line for the mutation in vcf file is:

V1 V2 V3 V4 V5 V6 V7
3772 chr15 90088606 . C T 160 PASS
V8
3772 SAMPLE=Horizon-CMP001;TYPE=SNV;DP=612;VD=28;AF=0.0458;BIAS=2:2;REFBIAS=369:215;VARBIAS=17:11;PMEAN=22.7;PSTD=1;QUAL=33.3;QSTD=1;SBF=0.84206;ODDRATIO=1.11034;MQ=60;SN=8.333;HIAF=0.0437;ADJAF=0.0033;SHIFT3=0;MSI=1;MSILEN=1;NM=1.1;HICNT=25;HICOV=572;LSEQ=CCTGGTCGCCATGGGCGTGC;RSEQ=TGCCAATGGTGATGGGCTTG;DUPRATE=0;SPLITREAD=0;SPANPAIR=0
V9 V10
3772 GT:DP:VD:AD:AF:RD:ALD 0/1:612:28:584,28:0.0458:369,215:17,11

Funcotator output for this specific mutation is (very long, but first 15 should be important):

Hugo_Symbol Chrom Start End_Position Strand Ref Tumor_Seq_Allele1 Alt
3772 IDH2 chr15 90088606 90088606 + C C T
AF DP Entrez_Gene_Id Center NCBI_Build Variant_Classification
3772 0.0458 612 3418 __UNKNOWN__ hg38 Intron
Variant_Type
3772 SNP
> h1.vardict[(h1.vardict$Hugo_Symbol=='IDH2' & h1.vardict$Start==90088606), ]
Hugo_Symbol Chrom Start End_Position Strand Ref Tumor_Seq_Allele1 Alt
3772 IDH2 chr15 90088606 90088606 + C C T
AF DP Entrez_Gene_Id Center NCBI_Build Variant_Classification
3772 0.0458 612 3418 __UNKNOWN__ hg38 Intron
Variant_Type dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode
3772 SNP 121913503 __UNKNOWN__
Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2
3772 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__
Tumor_Validation_Allele1 Tumor_Validation_Allele2
3772 __UNKNOWN__ __UNKNOWN__
Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2
3772 __UNKNOWN__ __UNKNOWN__
Verification_Status Validation_Status Mutation_Status Sequencing_Phase
3772 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__
Sequence_Source Validation_Method Score BAM_File Sequencer
3772 __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__
Tumor_Sample_UUID Matched_Norm_Sample_UUID Genome_Change
3772 __UNKNOWN__ __UNKNOWN__ g.chr15:90088606C>T
Annotation_Transcript Transcript_Strand Transcript_Exon
3772 ENST00000559482.5 - NA
Transcript_Position cDNA_Change Codon_Change Protein_Change
3772 c.e3+104G>A 
Other_Transcripts
3772 IDH2_ENST00000330062.8_Missense_Mutation_p.R172K|IDH2_ENST00000540499.2_Missense_Mutation_p.R120K
Refseq_mRNA_Id Refseq_prot_Id SwissProt_acc_Id SwissProt_entry_Id
3772 P48735 IDHP_HUMAN
Description UniProt_AApos
3772 isocitrate dehydrogenase (NADP(+)) 2, mitochondrial __UNKNOWN__
UniProt_Region UniProt_Site UniProt_Natural_Variations
3772 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__
UniProt_Experimental_Info
3772 __UNKNOWN__
GO_Biological_Process
3772 2-oxoglutarate metabolic process (GO:0006103)|carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)
GO_Cellular_Component
3772 extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)
GO_Molecular_Function
3772 isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)
COSMIC_overlapping_mutations
3772 p.R172K(281)|p.R172M(30)|p.R172fs*100(1)|p.R172T(2)|p.R172N(1)
COSMIC_fusion_genes
3772 
COSMIC_tissue_types_affected
3772 NS(223)|adrenal_gland(294)|autonomic_ganglia(349)|biliary_tract(876)|bone(893)|breast(1151)|central_nervous_system(11211)|cervix(20)|endometrium(22)|eye(81)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(26199)|kidney(260)|large_intestine(1302)|liver(111)|lung(320)|meninges(57)|oesophagus(176)|ovary(533)|pancreas(585)|perineum(1)|peritoneum(60)|pleura(11)|prostate(172)|salivary_gland(105)|skin(644)|small_intestine(26)|soft_tissue(479)|stomach(547)|testis(11)|thymus(26)|thyroid(239)|upper_aerodigestive_tract(127)|urinary_tract(32)|vulva(66)
COSMIC_total_alterations_in_gene Tumorscape_Amplification_Peaks
3772 47210 __UNKNOWN__
Tumorscape_Deletion_Peaks TCGAscape_Amplification_Peaks
3772 __UNKNOWN__ __UNKNOWN__
TCGAscape_Deletion_Peaks DrugBank ref_context gc_content
3772 __UNKNOWN__ ATGGGCGTGCCTGCCAATGGT 0.563591
CCLE_ONCOMAP_overlapping_mutations CCLE_ONCOMAP_total_mutations_in_gene
3772 __UNKNOWN__ __UNKNOWN__
CGC_Mutation_Type CGC_Translocation_Partner CGC_Tumor_Types_Somatic
3772 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__
CGC_Tumor_Types_Germline CGC_Other_Diseases
3772 __UNKNOWN__ __UNKNOWN__
DNARepairGenes_Activity_linked_to_OMIM FamilialCancerDatabase_Syndromes
3772 __UNKNOWN__ 
MUTSIG_Published_Results OREGANNO_ID OREGANNO_Values tumor_f t_alt_count
3772 __UNKNOWN__ 0.0458 28
t_ref_count n_alt_count n_ref_count
3772 584 NA NA
Gencode_34_secondaryVariantClassification Achilles_Top_Genes
3772 
ClinVar_VCF_AF_ESP ClinVar_VCF_AF_EXAC ClinVar_VCF_AF_TGP
3772 NA NA NA
ClinVar_VCF_ALLELEID
3772 362866

[GenoMax]

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