id String | Unique variant ID, this consists of chromosome, position, reference and alternate alleles in this format: chrom:pos:ref:alt |
names List<String> | Other IDs found for this genomic variant across all VCF files indexed |
chromosome String | The chromosome where the genomic variant is located |
start int | The 1-based position where the genomic variant starts. For variants coming from VCF files, this position is likely to be normalised, in this case, the original call in the file is stored in studies.files.call (see below) |
end int | The 1-based position where the genomic variant ends. For variants coming from VCF files, this position is likely to be normalised, in this case, the original call in the file is stored in studies.files.call (see below) |
reference String | Reference allele. For variants coming from VCF files, this position is likely to be normalised, in this case, the original call in the file is stored in studies.files.call (see below) |
alternate String | Alternate allele. For variants coming from VCF files, this position is likely to be normalised, in this case, the original call in the file is stored in studies.files.call (see below) |
strand String | Reference strand for this variant, by default all variants are represented 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 and Sequence Ontology (SO) terms 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 | NA | | SYMBOLIC | NA |
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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 and SO terms are: | 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 kist 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 identifier within the study. | sampleCount
int | Count of samples with non-missing genotypes in this variant from the cohort.
This value is used as denominator for genotypeFreq. | fileCount
int | Count of files with samples from the cohort that reported this variant.
This value is used as denominator for filterFreq. | alleleCount
int | Total number of alleles in called genotypeCounters. It does not include missing alleles.
This value is used as denominator for refAlleleFreq and altAlleleFreq. | refAlleleCount
int | Number of reference alleles found in this variant. | refAlleleFreq
float | Reference allele frequency calculated from refAlleleCount and alleleCount, in the range [0,1] | altAlleleCount
int | Number of main alternate alleles found in this variants. It does not include secondary alternates. | 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 genotypes with all alleles missing (e.g. ./.). It does not count partially missing genotypes like "./0" or "./1". | genotypeCount
Map<String, int> | Number of occurrences for each genotype.
This does not include genotype with all alleles missing (e.g. ./.), but it includes partially missing genotypes like "./0" or "./1".
Total sum of counts should be equal to the count of samples. | genotypeFreq
Map<String, float> | Genotype frequency for each genotype found calculated from the genotypeCount and samplesCount, in the range [0,1] | maf
float | Minor allele frequency. Frequency of the less common allele between the reference and the main alternate alleles.
This value does not take into acconunt secondary alternates. | mafAllele
String | Allele with minor frequency. | mgf
float | Minor genotype frequency. Frequency of the less common genotype seen in this variant.
This value takes into account all values from the genotypeFreq map. | mgfGenotype
String | Genotype with minor frequency. | filterCount
Map<String, int> | The number of occurrences for each FILTER value in files from samples in this cohort reporting this variant.
As each file can contain more than one filter value (usually separated by ';'), the total sum of counts could be greater than to the count of files. | filterFreq
Map<String, float> | Frequency of each filter calculated from the filterCount and filesCount, in the range [0,1] | qualityCount
int | The number of files from samples in this cohort reporting this variant with valid QUAL values.
This value is used as denominator to obtain the qualityAvg | qualityAvg
float | The average Quality value for files with valid QUAL values from samples in this cohort reporting this variant.
Some files may not have defined the QUAL value, so the sampling could be less than the filesCount. |
| 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 |
| sample SampleEntry | The sample information containing sampleId, fileIndex and data (see above) |
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| annotation | Variant Annotation object, this is a large data model and is documented independently |