Usually these results consists of huge text files.įor instance a file with all SNPs found between to plant varieties or with all SNPs found in a particular human individual would be a vcf file with thousands of lines. For reference, a second column is provided for genotyping assuming the site is polymorphic.In a lot of genomic analyses our troubles are not over once we get the results. One MAXGT sample column is provided for the normal genotyping (assuming the reference). The sample column gives the values specified in the FORMAT column. PhastCons – Denotes if the variant is an identical or similar sequence that occurs between species and maintained between species throughout evolution Format: AlleleFreqEVS|EVSCoverage|EVSSamplesĬosmic – The numeric identifier for the variant in the Catalogue of Somatic Mutations in Cancer (COSMIC) database ( .uk/cancergenome/projects/cosmic/).Ĭlinvar – Clinical significance from the ClinVar database ( Format: GlobalMinorAllele|AlleleFreqGlobalMinorĮVS – Allele frequency, sample count, and coverage taken from the Exome Variant Server (EVS). GMAF – Global minor allele frequency (GMAF) technically, the frequency of the second most frequent allele. The consequences are indicated using valid Sequence Ontology (SO) terms ( and typically are either regulatory_region_variant or TF_binding_site_variant.ĪF – The allele frequency from all populations of 1000 genomes dataĪA – The inferred allele ancestral to the chimpanzee/human lineage Many of the RegulatoryIDs begin with ENSR. The annotations provided in this field come from the Ensembl database of regulatory features even if RefSeq was selected as the annotation source. A comma-separated list for each affected regulatory region (including transcription factor binding sites) is provided using the following delimited format: RegulatoryID|Consequence. ĬSQR – Regulatory consequence as predicted by Variant Effect Predictor ( version 72.The consequences are indicated using valid Sequence Ontology (SO) terms ( If the selected annotation source was Ensembl, then the TranscriptIDs begin with ENST. If the annotation source selected was RefSeq, then many of the TranscriptIDs begin with NM_. Each entry in the list includes the HGNC gene symbol (when available), transcript ID, and functional consequences in a delimited format: HGNC|TranscriptID|Consequence. Ī comma-separated list for each affected gene is provided.This binary file can be loaded into VariantStudio for viewing see The ANT file contains consequences for all affected transcripts. Only canonical transcripts are included in the VCF file to maintain readability. ĬSQT – Transcript consequence as predicted by Variant Effect Predictor ( version 72.Illumina On-Node Annotation (IONA) provided annotations are: See VCF INFO Entries for possible entries. See VCF FORMAT Entries for possible entries. See VCF FILTER Entries for possible entries. Many variant callers assign quality scores (based on their statistical models) which are high relative to the error rate observed in practice. For example, the set of Q30 calls has a 0.1% error rate. For a quality score of Q, the estimated probability of an error is 10-(Q/10). Higher scores indicate higher confidence in the variant (and lower probability of errors). For example, an insertion of a single T can be represented as reference A and alternate AT.Ī Phred-scaled quality score assigned by the variant caller. The alleles that differ from the reference read. For example, a deletion of a single T can be represented as reference TT and alternate T. If no dbSNP entry exists at this position, the missing value ('.') is used. If there are multiple rs numbers at this location, the list is semicolon delimited. The rs number for the SNP obtained from dbSNP. For indels or deletions, this base is the reference base immediately before the variant. The convention for *.vcf files is that, for SNPs, this base is the reference base with the variant. The 1-based position of this variant in the reference chromosome. Chromosomes appear in the same order as the reference FASTA file (generally karyotype order). A description of the tags is also provided here and on Setting The header of the VCF file describes the tags used in the remainder of the file. The file naming convention for VCF files is as follows: SampleName_S#.vcf (where # is the sample number determined by ordering in the sample sheet). More information is available here: VCF File Format Each data line contains information about a single variant. The file format consists of meta-information lines, a header line, and then data lines.
VCF is a text file format that contains information about variants found at specific positions in a reference genome.