Documentation : Annotations Explained

Quality Information
StretchIs variant located in stretch of repetitive sequence, as indicated by GATK recent versions. Annotations Stretch_Unit and Stretch_Length give more information about the stretch
Stretch_UnitUnit of the stretch (e.g. GCC or T)
Stretch_LengthLength of the stretch on the present alleles.
AllelicRatioFraction of total reads called as alternative allele
Phred_PolymorphismThe Phred scaled probability of Probability that REF/ALT polymorphism exists at this site given sequencing data. Because the Phred scale is -10 * log(1-p), a value of 10 indicates a 1 in 10 chance of error, while a 100 indicates a 1 in 10^10 chance. The GATK values can grow very large when lots of NGS data is used to call.
Phred_GenotypeThe Genotype Quality, as a Phred-scaled confidence at the true genotype is the one provided in GT. In diploid case, if GT is 0/1, then GQ is really L(0/1) / (L(0/0) + L(0/1) + L(1/1)), where L is the likelihood of the NGS sequencing data under the model of that the sample is 0/0, 0/1/, or 1/1.
GenotypeObserved genotype, homozygous or heterozygous
Ref_Allele_DepthNumber of reads passing GATK quality threshold, with the reference allele
Alt_Allele_DepthNumber of reads passing GATK quality threshold, with the alternative allele
Quality_By_DepthVariant confidence (given as (AB+BB)/AA from the PLs) / unfiltered depth. (PL : phred-scaled likelyhood of the genotype). Low scores are indicative of false positive calls and artifacts. Note that QualByDepth requires sequencing reads associated with the samples with polymorphic genotypes.
Mapping_QualityRoot Mean Square of the mapping quality of the reads across all samples.
Base_Quality_Rank_SumThe u-based z-approximation from the Mann-Whitney Rank Sum Test for base qualities (ref bases vs. bases of the alternate allele). Note that the base quality rank sum test can not be calculated for homozygous sites.
Mapping_Quality_Rank_SumThe u-based z-approximation from the Mann-Whitney Rank Sum Test for mapping qualities (reads with ref bases vs. those with the alternate allele) Note that the mapping quality rank sum test can not be calculated for homozygous sites.
Read_Position_Rank_SumThe u-based z-approximation from the Mann-Whitney Rank Sum Test for the distance from the end of the read for reads with the alternate allele; if the alternate allele is only seen near the ends of reads this is indicative of error. Note that the read position rank sum test can not be calculated for homozygous sites.
Strand_BiasHow much evidence is there for Strand Bias (the variation being seen on only the forward or only the reverse strand) in the reads? Higher SB values denote more bias (and therefore are more likely to indicate false positive calls).
Fisher_Strand_BiasPhred-scaled p-value using Fisher's Exact Test to detect strand bias (the variation being seen on only the forward or only the reverse strand) in the reads. More bias is indicative of false positive calls. Note that the fisher strand test may not be calculated for certain complex indel cases or for multi-allelic sites.
VQSLODVQSLOD is the log odds ratio of being a true variant versus being false under the trained Gaussian mixture model when Variant Recalibration is applied.
DeltaPLThis field provides the likelihoods of the given genotypes (here, 0/0, 0/1, and 1/1). These are normalized, Phred-scaled likelihoods for each of the 0/0, 0/1, and 1/1, without priors. To be concrete, for the heterozygous case, this is L(data given that the true genotype is 0/1). The most likely genotype (given in the GT field) is scaled so that it's P = 1.0 (0 when Phred-scaled), and the other likelihoods reflect their Phred-scaled likelihoods relative to this most likely genotype
Tranches_FilterValue in the VCF Filter Column. Mainly used by GATK Variant Recalibration.
RBQAverage quality of reference-supporting bases (qual1)
ABQAverage quality of variant-supporting bases (qual2)
PhredFisherPPred-scaled P-value from Fisher's Exact Test
Genomic_SuperDups_ScoreSimilarity of the SegDup region to the alternate location region. See UCSC table description for details.
Genomic_SuperDups_LocationAlternate location of the SegDup region. See UCSC table description for details.
 

Population_Frequency Information
1000g2012apr_allDeprecatedalternative allele frequency data in 1000 Genomes Project for ALL populations
1000g2012apr_afrDeprecatedalternative allele frequency data in 1000 Genomes Project for African population
1000g2012apr_asnDeprecatedalternative allele frequency data in 1000 Genomes Project for Asian population
1000g2012apr_amrDeprecatedalternative allele frequency data in 1000 Genomes Project for admixed American population
1000g2012apr_eurDeprecatedalternative allele frequency data in 1000 Genomes Project for European population
1000g2014oct_allDeprecatedalternative allele frequency data in 1000 Genomes Project for ALL populations. Based on 201409 collection v5 (based on 201305 alignment) but including chrX and chrY data finally. ANNOVAR specific version with better indel matching.
1000g2014oct_afrDeprecatedalternative allele frequency data in 1000 Genomes Project for African population. Based on 201409 collection v5 (based on 201305 alignment) but including chrX and chrY data finally. ANNOVAR specific version with better indel matching.
1000g2014oct_easDeprecatedalternative allele frequency data in 1000 Genomes Project for East-Asian population. Based on 201409 collection v5 (based on 201305 alignment) but including chrX and chrY data finally. ANNOVAR specific version with better indel matching.
1000g2014oct_sasDeprecatedalternative allele frequency data in 1000 Genomes Project for South-Asian population. Based on 201409 collection v5 (based on 201305 alignment) but including chrX and chrY data finally. ANNOVAR specific version with better indel matching.
1000g2014oct_amrDeprecatedalternative allele frequency data in 1000 Genomes Project for admixed American population. Based on 201409 collection v5 (based on 201305 alignment) but including chrX and chrY data finally. ANNOVAR specific version with better indel matching.
1000g2014oct_eurDeprecatedalternative allele frequency data in 1000 Genomes Project for European population. Based on 201409 collection v5 (based on 201305 alignment) but including chrX and chrY data finally. ANNOVAR specific version with better indel matching.
esp5400_allDeprecatedalternative allele frequency in all subjects in the NHLBI-ESP project with 5400 exomes
esp5400_eaDeprecatedalternative allele frequency in European Americans in the NHLBI-ESP project with 5400 exomes
esp5400_aaDeprecatedalternative allele frequency in African Americans in the NHLBI-ESP project with 5400 exomes
esp6500_allalternative allele frequency in all subjects in the NHLBI-ESP project with 6500 exomes, including the indel calls and the chrY calls
esp6500_eaalternative allele frequency in European Americans in the NHLBI-ESP project with 6500 exomes, including the indel calls and the chrY calls
esp6500_aaalternative allele frequency in African Americans in the NHLBI-ESP project with 6500 exomes, including the indel calls and the chrY calls
ExAC_v02DeprecatedAlternative allele frequency in ALL populations in the ExAC 65.000 exomes database. Note that these are not all healthy individuals. Although values are similar, there are discrepancies between ANNOVAR ALL_population frequencies (used here) and the data available online. This is due to ANNOVAR using raw allele counts, versus the ExAC Browser using adjusted allele counts (DP >= 10 & GQ >= 20)
ExAC_v03_AF_ALLAlternative allele frequency in ALL populations in the ExAC 65.000 exomes database. Note that these are not all healthy individuals. Although values are similar, there are discrepancies between ANNOVAR ALL_population frequencies (used here) and the data available online. This is due to ANNOVAR using raw allele counts, versus the ExAC Browser using adjusted allele counts (DP >= 10 & GQ >= 20)
ExAC_v03_AN_ALLTotal Chromosome Count in ALL populations in the ExAC 65.000 exomes database for this variant. Only chromosomes used in variant calling are counted, discarding non-covered samples.
ExAC_v03_AF_AFRAlternative allele frequency in AFR population in the ExAC 65.000 exomes database. Note that these are not all healthy individuals. Although values are similar, there are discrepancies between ANNOVAR AFR_population frequencies (used here) and the data available online. This is due to ANNOVAR using raw allele counts, versus the ExAC Browser using adjusted allele counts (DP >= 10 & GQ >= 20)
ExAC_v03_AN_AFRTotal Chromosome Count in AFR population in the ExAC 65.000 exomes database for this variant. Only chromosomes used in variant calling are counted, discarding non-covered samples.
ExAC_v03_AF_AMRAlternative allele frequency in AMR population in the ExAC 65.000 exomes database. Note that these are not all healthy individuals. Although values are similar, there are discrepancies between ANNOVAR AMR_population frequencies (used here) and the data available online. This is due to ANNOVAR using raw allele counts, versus the ExAC Browser using adjusted allele counts (DP >= 10 & GQ >= 20)
ExAC_v03_AN_AMRTotal Chromosome Count in AMR population in the ExAC 65.000 exomes database for this variant. Only chromosomes used in variant calling are counted, discarding non-covered samples.
ExAC_v03_AF_EASAlternative allele frequency in EAS population in the ExAC 65.000 exomes database. Note that these are not all healthy individuals. Although values are similar, there are discrepancies between ANNOVAR EAS_population frequencies (used here) and the data available online. This is due to ANNOVAR using raw allele counts, versus the ExAC Browser using adjusted allele counts (DP >= 10 & GQ >= 20)
ExAC_v03_AN_EASTotal Chromosome Count in EAS population in the ExAC 65.000 exomes database for this variant. Only chromosomes used in variant calling are counted, discarding non-covered samples.
ExAC_v03_AF_FINAlternative allele frequency in FIN population in the ExAC 65.000 exomes database. Note that these are not all healthy individuals. Although values are similar, there are discrepancies between ANNOVAR FIN_population frequencies (used here) and the data available online. This is due to ANNOVAR using raw allele counts, versus the ExAC Browser using adjusted allele counts (DP >= 10 & GQ >= 20)
ExAC_v03_AN_FINTotal Chromosome Count in FIN population in the ExAC 65.000 exomes database for this variant. Only chromosomes used in variant calling are counted, discarding non-covered samples.
ExAC_v03_AF_NFEAlternative allele frequency in NFE population in the ExAC 65.000 exomes database. Note that these are not all healthy individuals. Although values are similar, there are discrepancies between ANNOVAR NFE_population frequencies (used here) and the data available online. This is due to ANNOVAR using raw allele counts, versus the ExAC Browser using adjusted allele counts (DP >= 10 & GQ >= 20)
ExAC_v03_AN_NFETotal Chromosome Count in NFE population in the ExAC 65.000 exomes database for this variant. Only chromosomes used in variant calling are counted, discarding non-covered samples.
ExAC_v03_AF_OTHAlternative allele frequency in OTH population in the ExAC 65.000 exomes database. Note that these are not all healthy individuals. Although values are similar, there are discrepancies between ANNOVAR OTH_population frequencies (used here) and the data available online. This is due to ANNOVAR using raw allele counts, versus the ExAC Browser using adjusted allele counts (DP >= 10 & GQ >= 20)
ExAC_v03_AN_OTHTotal Chromosome Count in OTH population in the ExAC 65.000 exomes database for this variant. Only chromosomes used in variant calling are counted, discarding non-covered samples.
ExAC_v03_AF_SASAlternative allele frequency in SAS population in the ExAC 65.000 exomes database. Note that these are not all healthy individuals. Although values are similar, there are discrepancies between ANNOVAR SAS_population frequencies (used here) and the data available online. This is due to ANNOVAR using raw allele counts, versus the ExAC Browser using adjusted allele counts (DP >= 10 & GQ >= 20)
ExAC_v03_AN_SASTotal Chromosome Count in SAS population in the ExAC 65.000 exomes database for this variant. Only chromosomes used in variant calling are counted, discarding non-covered samples.
Kaviar_150923_AFAlternate allele frequency in kaviar database, release 2015-09-23.
Kaviar_150923_ANTotal Chromosome Count in kaviar database, release 2015-09-23. Only chromosomes used in variant calling are counted, discarding non-covered samples.
snp130_rsIDDeprecatedSNP-IDs for variants present in dbSNP.v130. No allele Frequencies
snp135_rsIDDeprecatedSNP-IDs for variants present in dbSNP.v135.
snp135_MAFDeprecatedMinor Allele Frequency for variants present in dbSNP.v135.
snp135_NrChrDeprecatedNumber of Chromosomes in dbSNP to base the Minor Allele Frequency on.
snp135_ClinicalDeprecatedAre snps marked as clinically associated? 1 for true, zero for false.
snp137_rsIDDeprecatedSNP-IDs for variants present in dbSNP.v137.
snp137_MAFDeprecatedMinor Allele Frequency for variants present in dbSNP.v137.
snp137_NrChrDeprecatedNumber of Chromosomes in dbSNP to base the Minor Allele Frequency on.
snp137_ClinicalDeprecatedAre snps marked as clinically associated? 1 for true, zero for false.
snp138_rsIDSNP-IDs for variants present in dbSNP.v138. ANNOVAR specific version is used for better indel matching
snp138_MAFMinor Allele Frequency for variants present in dbSNP.v138. ANNOVAR specific version is used for better indel matching
snp138_NrChrNumber of Chromosomes in dbSNP to base the Minor Allele Frequency on.
snp138_ClinicalAre snps marked as clinically associated? 1 for true, zero for false.
snp142_rsIDSNP-IDs for variants present in dbSNP.v142. ANNOVAR specific version is used for better indel matching
snp142_MAFMinor Allele Frequency for variants present in dbSNP.v142. ANNOVAR specific version is used for better indel matching
snp142_NrChrNumber of Chromosomes in dbSNP to base the Minor Allele Frequency on.
snp142_ClinicalAre snps marked as clinically associated? 1 for true, zero for false.
 

Gene_Information Information
Ensembl_VariantType
Ensembl_GeneLocation
Ensembl_cPointAA
Ensembl_cPointNT
Ensembl_GeneID
Ensembl_TranscriptID
Ensembl_Exon
RefSeq_VariantType
RefSeq_GeneLocation
RefSeq_cPointAA
RefSeq_cPointNT
RefSeq_Symbol
RefSeq_Transcript
RefSeq_Exon
RefSeq_Protein_Length_Difference
UCSC_VariantType
UCSC_GeneLocation
UCSC_cPointAA
UCSC_cPointNT
UCSC_Symbol
UCSC_Transcript
UCSC_Exon
EffectEffect of the Variant on protein (Non-Synonymous, frameshift, UTR, ...)
Effect_ImpactImpact class : high, moderate, modifier, unknown
Functional_ClassMore detailed effect on coding variant: missensen, silent, ...
Gene_Symbol
Gene_ExonExon or Intron number. Numbering starts from 1.
Codon_ChangeFor exonic variants: The affected codon sequences for WT and MUT. For intronic/downstream variants : distance to the nearest exon.
Amino_Acid_Changep.Point notation of protein alteration.
Gene_TranscriptTranscript reference for the listed data.
Gene_CodingIs the affected gene coding or non-coding
Transcript_BioTypeType of the gene (protein_coding,miRNA,pseudogene,...)
 

Splice_Prediction Information
scsnv11_ADAEnsemble splice alteration prediction, using Adaptive boosting, based on PWM, MaxEntScan, NNSplice and HSF. pmid: 25416802. Score represents probability of altered spicing (0-1), proposed cutoff is 0.6
scsnv11_RFEnsemble splice alteration prediction, using random forest classification, based on PWM, MaxEntScan, NNSplice and HSF. pmid: 25416802. Score represents probability of altered spicing (0-1), proposed cutoff is 0.6
spidex_dPSILicense: deepgenomicsDeep Learning prediction of alternate splicing. deltaPSI is the maximal predicted difference in splicing over 12 tissues. This annotation source is only available for non-profic, academic users. Please send a signed copy of the EULA to activate it.
spidex_ZscoreLicense: deepgenomicsDeep Learning prediction of alternate splicing. Zscore is a ranking of the observed value among all predictions. Assuming normal distribution, this rank can be represented as a Zscore. Lower tail represents reduced splicing, upper tail represents a new splice site. This annotation source is only available for non-profic, academic users. Please send a signed copy of the EULA to activate it.
 

Pathogenicity_Prediction Information
ljb_LRTDeprecatedRescaled (0-1) likelihood ratio test of codon constrained. Higher score for more constrained codons. See dbNSFP paper for details (pmid: 21520341)
ljb_MutTastDeprecatedMutation Taster has four categories: (A)utomatic and (D)isease causing, for which the score is p-value for a true prediction. (N)on-deleterious and (P)olymorphism known, for which the score is 1 - p-value for a true prediction. The higher the score, the more likely the variant is deleterious. See dbNSFP paper for details (pmid: 21520341)
ljb_PhyloPDeprecatedRescaled (0-1) PhyloP score. Higher Score for more conserved sites. Prediction is Rescaled Score higher than 0.95 for a conserved site. See dbNSFP paper for details (pmid: 21520341)
ljb_PolyPhen2DeprecatedPolyphen2 Scores. (D)amaging if over 0.85, (P)ossibly damaging if over 0.15, (B)enign otherwise. See dbNSFP paper for details (pmid: 21520341)
ljb_SiftDeprecated1 - sift scores. Damaging if over 0.95. See dbNSFP paper for details (pmid: 21520341)
ljb_GERPDeprecatedConservation Scores. Exact method to be added. High score is indicative of constrained site. (See Davidov et al, 2010, plos computational biology)
CADD_rawCADD C-Scores. Integrated pathogenicity predication score. Raw Scores, see publication for details.
CADD_phredCADD C-Scores in Phred Scale. E.g.: Scores above 20 are in the 1% top scoring variants, scores above 30 are in the 0.1% top scoring variants.
ljb26_SIFTDeprecatedToDo
ljb26_pp2_hdivDeprecatedToDo
ljb26_pp2_hvarDeprecatedToDo
ljb26_LRTDeprecatedToDo
ljb26_MutationTasterDeprecatedToDo
ljb26_MutationAssessorDeprecatedToDo
ljb26_FATHMMDeprecatedToDo
ljb26_RadialSVMDeprecatedToDo
ljb26_LRDeprecatedToDo
ljb26_VEST3DeprecatedToDo
ljb26_CADD_phredDeprecatedToDo
ljb26_GERP_RSDeprecatedToDo
ljb26_PhyloP46DeprecatedToDo
ljb26_PhyloP100DeprecatedToDo
ljb26_SiPhyDeprecatedToDo
dbnsfp30a_SIFTToDo
dbnsfp30a_pp2_hdivToDo
dbnsfp30a_pp2_hvarToDo
dbnsfp30a_LRTToDo
dbnsfp30a_MutationTasterToDo
dbnsfp30a_MutationAssessorToDo
dbnsfp30a_FATHMMToDo
dbnsfp30a_PROVEANToDo
dbnsfp30a_MetaSVMToDo
dbnsfp30a_MetaLRToDo
dbnsfp30a_VEST3ToDo
dbnsfp30a_CADD_phredToDo
dbnsfp30a_DANN_ScoreToDo
dbnsfp30a_GERP_RSToDo
dbnsfp30a_fathmm_mklToDo
dbnsfp30a_fitConsIntegrated FitCons Score (confidence)
dbnsfp30a_PhyloP7ToDo
dbnsfp30a_PhyloP20ToDo
dbnsfp30a_phastCons7ToDo
dbnsfp30a_phastCons20ToDo
dbnsfp30a_SiPhyToDo
MutationTasterMutation Taster has four categories: (A)utomatic and (D)isease causing, for which the score is p-value for a true prediction. (N)on-deleterious and (P)olymorphism known, for which the score is 1 - p-value for a true prediction. The higher the score, the more likely the variant is deleterious. See Mutation Taster Website for details. These values are queried using the MTQE interface, and should be more complete than Annovar scores. Missing values reflect intronic and exotic alleles and should be checked manually
SIFT_Score1 - SIFT scores, similar to ANNOVAR scale. Damaging if over 0.95.
SIFT_EffectSIFT Effect prediction. (T)olerated, (D)eleterious are native SIFT predictions. If no prediction was possible, a dot (.) is returned. Frameshift and nonsense mutations are annotated with an asterisk (*).
PROVEAN_ScorePROVEAN Score. A novel prediction from the authors of SIFT. They use a cut-off of -2.5 as threshold for damaging mutations.
PROVEAN_EffectPROVEAN Effect prediction. (N)eutral, (D)amaging are native PROVEAN predictions. If no prediction was possible, a dot (.) is returned. Frameshift and nonsense mutations are annotated with an asterisk (*).
SIFT_ProteinSIFT/PROVEAN predictions are transcript specific. Ensembl protein IDs are used to indicate transcript
SIFT_PositionSIFT/PROVEAN predictions are transcript specific. This annotation indicates the altered AA position in the transcript.
SIFT_TypeAlteration type predicted by SIFT/PROVEAN
SIFT_AA_ChangeAmino Acid change predicted by SIFT/PROVEAN
Grantham_ScoreGrantham score for the AA change predicted by SIFT/PROVEAN
 

Clinical Information
SNV_LinkLink to the ClinVar page. ClinVar is designed to provide a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence (Single Nucleotide Variant Entries).
SNV_MatchClinVar Match Type. ClinVar holds both single nucleotide variants and copy number variations. Only SNV variants can have exact matches. Exact matches are defined as same position, same reference and alternate alleles. All other matches, such as SNV inside a ClinVar CNV, or indel spanning a ClinVar SNV, are labeled as overlapping variants (Single Nucleotide Variant Entries)
SNV_AA_MatchClinVar Match Type at Amino Acid level. ClinVar holds both single nucleotide variants and copy number variations. Only SNV variants can have exact matches. Exact matches are defined variants leading to the same amino-acid change. All other matches, such as SNV inside a ClinVar CNV, or indel spanning a ClinVar SNV, are labeled as overlapping variants (Single Nucleotide Variant Entries)
SNV_GeneGeneSymbol listed as the affected gene in ClinVar (Single Nucleotide Variant Entries).
SNV_NM_idRefSeq Transcript listed as the affected gene in ClinVar. For many variants, this information was not provided. In case of multiple transcripts, these values are very prone to errors (Single Nucleotide Variant Entries)!
SNV_NP_idRefSeq Protein listed as the affected protein in ClinVar. This might be ambigous or incorrect in case of a ClinVar CNV matching a sample SNV. For many variants, this information was not provided. In case of multiple transcripts, these values are very prone to errors!
SNV_EffectEffect on Protein as listed in ClinVar. For many variants, this information was not provided. In case of multiple transcripts, these values are very prone to errors (Single Nucleotide Variant Entries)!
SNV_Last_UpdateTime Stamp of the latest update to this variant in ClinVar (Single Nucleotide Variant Entries).
SNV_DiseaseDisease associated to the variant (Single Nucleotide Variant Entries).
SNV_ClassClassification with regard to pathogenicity (Single Nucleotide Variant Entries).
SNV_Class_CommentComments about classification with regard to pathogenicity (Single Nucleotide Variant Entries).
SNV_XRef_AlleleVariant-oriented links to external databases (Single Nucleotide Variant Entries).
SNV_XRef_GeneGene-oriented links to external databases (Single Nucleotide Variant Entries).
SNV_XRef_DiseaseDisease-oriented links to external databases. Benign variants are labeled as 'AllHighlyPenetrant' (Single Nucleotide Variant Entries).
SNV_PubMedLink to Pubmed with articles related to the variant (Single Nucleotide Variant Entries).
 

Gene_Ontology Information
GO_IDGO_ID for terms associated to a gene, based on gene2go from ncbi. SNP_to_GeneID is taken from snpEff annotations for Effects that are NOT downstream,intergenic,none,upstream.
GO_TermGO Terms associated to a gene, based on gene2go from ncbi. SNP_to_GeneID is taken from snpEff annotations for Effects that are NOT downstream,intergenic,none,upstream..
GO_Term_TypeGO Term type: Biological Process, cellular Component, molecular function
GO_Obsolete0/1 : Within GO, terms are sometimes replaced by other terms. Old terms are kept as reference, but should no longer be used. This annotation indicates if a term has been replaced.
GO_First_Level_Parent_IDsGene Ontology ID, one-level up the hierarchy. This is slow!
GO_First_Level_Parent_NamesGene Ontology ID, one-level up the hierarchy. This is slow!
 

User_Defined Information
Panel_DefinitionIf Variant affects a gene in a gene panel, list the name of the panel
Panel_DescriptionIf Variant affects a gene in a gene panel, list the name of the panel
Panel_GeneGene Panel entry, hit by the variant. Taken from ANNOVAR_refgene
Panel_Gene_CommentGene specific comments from the GenePanel entry. User Provided info
 

Oncology Information
Genotype_RatioAllelic Ratio, as called by GATK Genotyper. This is 0/0.5/1 for diploid samples, but can be informative for samples of high ploidy.
PloidySample Ploidy used during genotyping. By default, this is two. Use this value to interpret the Genotype Ratio.
Somatic_StateSomatic State of the variant. Only informative for MuTect/VarScan imports. States are 0:reference, 1:germline, 2:somatic, 3:LOH, 4:post-translational, 5:unknown.
COSMICv70_ID
COSMICv70_Tissue
COSMICv70_Occurence
 

Custom_VCF_Fields Information