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id String | Unique variant ID, the format is chrom:pos:ref:alt |
names List<String> | Other IDs used for this genomic variation across all VCF files indexed |
chromosome String | The chromosome where the genomic variation occurred |
start int | The normalised position where the genomic variation starts |
end int | The normalised position where the genomic variation ends |
reference String | Reference allele |
alternate String | Alternate allele |
strand String | Reference strand for this variant, by default all variants are expressed in the positive strand |
length int | Length of the genomic variation, which depends on the variant type |
type VariantType | Type of variant, the accepted types are: SNV | SO:0001483 | SNP | SO:0000694 | MNV | SO:0002007 | MNP | SO:0001013 | INDEL | SO:1000032 | INSERTION | SO:0000667 | DELETION | SO:0000159 | TRANSLOCATION | SO:0000199 | INVERSION | SO:1000036 | CNV | SO:0001019 | DUPLICATION | SO:1000035 | BREAKEND |
| SYMBOLIC |
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sv StructuralVariation | Specific information for Structural Variants ciStartLeft int | The confidence interval around START for imprecise variants - left | ciStartRight int | The confidence interval around START for imprecise variants - right
| ciEndLeft int | The confidence interval around END for imprecise variants - left
| ciEndRight int | The confidence interval around END for imprecise variants - right
| copyNumber int | Number of copies for CNV variants | leftSvInsSeq String | Left inserted sequence for long INSERTIONS | rightSvInsSeq String | Right inserted sequence for long INSERTIONS | type StructuralVariantType | Structural variant types: COPY_NUMBER_GAIN | SO:0001742 | COPY_NUMBER_LOSS | SO:0001743 | TANDEM_DUPLICATION | SO:1000173 |
| breakend Breakend | mate BreakendMate | chromosome | The chromosome of the mate variant | position | The position of the mate variant | ciPositionLeft | The confidence interval around BREAKEND position - left | ciPositionRight | The confidence interval around BREAKEND position - right |
| orientation BreakendOrientation | SE | Start - End t[p[ piece extending to the right of p is joined after t | SS | Start - Start t]p] reverse comp piece extending left of p is joined after t | ES | End - Start ]p]t piece extending to the left of p is joined before t | EE | End - End [p[t reverse comp piece extending the right of p is joined before t |
| insSeq String | Sequence inserted between the two breakends |
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studies List<StudyEntry> | Information specific to each study the variant was read from, such as samples or statistics studyId String | Unique ID for the study | secondaryAlternates List<AlternateCoordinate> | All alternate alleles that have been indexed along with a variant alternate chromosome String | The chromosome where the genomic variation occurred | start int | First position 1-based of the alternate | end int | End position 1-based of the alternate | reference String | Reference allele | alternate String | Alternate allele | type VariantType | Type of variant |
| files List<FileEntry> | List of files from the study where the variant was present fileId String | Unique ID of the indexed file | call OriginalCall | Original call in the VCF file, this is filled when the variant has been normalised variantId | Original call position for the variant, if the file was normalised. | alleleIndex | Alternate allele index of the original multi-allellic variant call |
| data Map<String, String> | File related data that depend on the format of the file the variant was initially read from. |
| sampleDataKeys List<String> | Specifies the sample data keys for each sample data (see below). The first key is always genotype (GT). | samples List<SampleEntry> | Sample-related data, each element is related to one sample and contains the specific information for one sample sampleId String | Unique sample ID | fileIndex int | The relative index position in files where this sample was loaded | data List<String> | Sample data, field GT is always the first one. The order and length must match sampleDataKeys field |
| stats List<VariantStats> | Variant stats for each variant in the different cohorts, it contains the following fields: cohortId String | Unique cohort ID | alleleCount int | Total number of alleles in called genotypeCounters. Does not include missing alleles | refAlleleCount int | Number of reference alleles found in this variant | altAlleleCount int | The number of main alternate alleles found in these variants excluding secondary alternates | refAlleleFreq float
| Reference allele frequency calculated from refAlleleCount and alleleCount, in the range (0,1) | altAlleleFreq float | Alternate allele frequency calculated from altAlleleCount and alleleCount, in the range (0,1) | missingAlleleCount int | Number of missing alleles | missingGenotypeCount int | Number of missing genotypeCounters | genotypeCount Map<String, int> | Count for each genotype found | genotypeFreq Map<String, float> | Genotype frequency for each genotype found | filterCount Map<String, int> | Number of samples with non-missing genotype with that specific filter | filterFreq Map<String, float> | Frequency of each filter. Count divided by the number of non-missing samples | qualityAvg float | The weighted average of the Quality computed only for non-missing samples | maf float | Minor allele frequency | mgf float | Minor genotype frequency | mafAllele String | The allele with minor frequency | mgfGenotype String | Genotype with minor frequency |
| scores List<VariantScore> | Analysis scores such as GWAS precomputed and indexed id String | Variant score ID | cohort1 String | The main cohort used for calculating this score | cohort2 String | The optional secondary cohort used for calculating the score | score float | Score value | pValue float | Score p-value |
| issues List<IssueType> | Issues found in this variant for a specific sample in this study type IssueType | Issues can have one of these types DUPLICATION |
| DISCREPANCY |
| MENDELIAN_ERROR |
| DE_NOVO |
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| sample SampleEntry | The sample information containing sampleId, fileIndex and data (see above) |
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annotation | Variant annotation object |