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Overview

The main goal for indexing variant data into OpenCGA Storage is to be able to make queries and extract this data in a efficient way. There are different alternatives ways to access to the data (via CLI, RESTful , Java API, Python API, ...) and multiple implementations of the VariantStorageManager (OpenCGA Storage MongoDB, OpenCGA Storage Hadoop, ...).

All this layers and implementations will use the same specification defined in this document.

There are defined an small set of READ-ONLY methods to achieve all the required functionality.

  • Query: Return all variants that matches with a given query
  • Count: Count the result of a given query
  • Aggregation Stats: Group variants by some field, you can count by region with this query.

Query Parameters

A filter is a pair of <key>, <value>, where the keys are predefined, and the values are defined by the user, using an specific format. In the next sections, all this keys are going to be enumerated, explaining their effect and the required format of the value.

There are some general rules that are applied for every case:The API described here fetches the sample data from a variant

  1. Returned variants will match positively with all the filters, except with the positional filters. Variants will need to match with, at least, one positional filter (if any).

    The positional parameters are:

    • region
    • id
    • gene
    • panel
    • xref
  2. When a filter accepts a list of values, the filter can be configured to pass ALL filters or ANY filter depending on the separator:

    • ANY: (Comma "," separator) The filter will be valid if the variant passes ANY of the filters.
      Define an OR operation between the elements in the query.
      Example: "type : SNV,INDEL"  :  Variants of type SNV OR INDEL
    • ALL: (Semicolon ";" separator) The filter will be valid if the variant passes ALL filters.
      Define an AND operation between the separated elements
      Example: "study : study1;study2"  :  Variants present in study1 AND in study2

So, the query ct: missense_variant,stop_lost will return all variants that are either missense_variant, stop_lost or both, but ct: missense_variant;stop_lost will return variants that are at the same time, missense_variant and stop_lost (in two different overlapping transcripts).

Genomic Parameters

This general filters will match with fields from the VCF input files.

All this parameters are positive filters. The output will contain variants that match with this filters

Parameter

Description

Example

id

List of IDs, these can be rs IDs (dbSNP) or variants in the format chrom:start:ref:alt,

rs116600158

COSM6350960

19:7177679:C:T

region

List of regions, these can be just a single chromosome name or regions in the format <chromosome>:<start>-<end>

chr22

3:100000-200000

type

List of types, accepted values are SNV, MNV, INDEL, SV, CNV, INSERTION, DELETION,

SNV,INDEL

gene

List of genes, most gene IDs are accepted (HGNC, Ensembl gene, ...).

This is an alias to 'xref' parameter.

When used together with ct, biotype or transcriptFlag, all filters will need to match within the same transcript.

BRCA2

BMPR

ENSG00000174173

ENST00000495642

panel

Filter by genes from the given disease panel


xref

List of any external reference, these can be genes, proteins or variants. Accepted IDs include HGNC, Ensembl genes, dbSNP, ClinVar, HPO, Cosmic, ...

BRCA2

ENST00000495642

COSM6350960

VAR_057355

rs116600158


Sample and Family Parameters

Parameter

Description

Example

project

Project [user@]project where project can be either the ID or the alias

 

study

Filter variants from the given studies, these can be either the numeric ID or the alias with the format user@project:study

 

sample

Filter variants where the samples contain the variant (HET or HOM_ALT).

Accepts AND ( ; ) and OR ( , ) operators.

This will automatically set 'includeSample' parameter when not provided

HG0097,HG00978

genotype

Samples with a specific genotype: 

{samp_1}:{gt_1}(,{gt_n})*(;{samp_n}:{gt_1}(,{gt_n})*)*

Unphased genotypes (e.g. 0/1, 1/1) will also include phased genotypes (e.g. 0|1, 1|0, 1|1), but not vice versa.

Genotype aliases accepted: HOM_REF, HOM_ALT, HET, HET_REF, HET_ALT and MISS

This will automatically set 'includeSample' parameter when not provided

HG0097:0/0;HG0098:0/1,1/1

HG0097:HOM_REF;HG0098:HET_REF,HOM_ALT

sampleAnnotation

Selects some samples using metadata information from Catalog.

age>20;phenotype=hpo:123,hpo:456;name=smith

format

Filter by any FORMAT field from samples. [{sample}:]{key}{op}{value}[,;]*.

If no sample is specified, will use all samples from "sample" or "genotype" filter.

Many FORMAT fields can be combined.

DP>200

HG0097:DP>200,HG0098:DP<10 .

HG0097:DP>200;GT=1/1,0/1,HG0098:DP<10

file

Filter variants from the files specified.

This will set includeFile parameter when not provided

 

info

Filter by INFO attributes from file. [{file}:]{key}{op}{value}[,;]* 

If no file is specified, will use all files from "file" filter.

Many INFO fields can be combined.

AN>200

file_1.vcf:AN>200;file_2.vcf:AN<10

file_1.vcf:AN>200;DB=true;file_2.vcf:AN<10

filter

Specify the FILTER for any of the files.

If 'file' filter is provided, will match the file and the filter.

PASS,LowGQX

qual

Specify the QUAL for any of the files.

If 'file' filter is provided, will match the file and the qual.

>123.4

family

Filter variants where any of the samples from the given family contains the variant (HET or HOM_ALT)

 

familyMembers

Sub set of the members of a given family

 

familyDisorder

Specify the disorder to use for the family segregation

 

familySegregation

Filter by mode of inheritance from a given family. Accepted values: [ monoallelic, monoallelicIncompletePenetrance, biallelic, biallelicIncompletePenetrance, XlinkedBiallelic, XlinkedMonoallelic, Ylinked, MendelianError, DeNovo, CompoundHeterozygous ]

 

Cohort Stats Parameters

Apart from the data provided on the files, there are some statistics calculated from the genotypes, or parsed from the INFO column, if the input was an aggregated file.

This filters are related with the statistics from a specific study and cohort. Knowing that, the format will be the same for each filter: <study>:<cohort><comparator><value>, where the available comparators are: <, <=, >, >=, = and !=.

Parameter

Description

Example

cohort

Select variants with calculated stats for the selected cohorts

 

cohortStatsRef

Reference Allele Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}.

ALL>0.6

cohortStatsAlt

Alternate Allele Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}.

ALL<=0.4

cohortStatsMaf

Minor Allele Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}.

study:ALL<0.01

cohortStatsMgf

Minor Genotype Frequency: [{study:}]{cohort}[<|>|<=|>=]{number}.

COH1<0.1,COH2<0.3


Variant Annotation Parameters

Parameter

Description

Example

biotype

List of biotypes,

When used together with gene, ct or transcriptFlag, all filters will need to match within the same transcript.

protein_coding

ct

List of SO consequence types,

When used together with gene, biotype or transcriptFlag, all filters will need to match within the same transcript.

missense_variant,stop_lost

SO:0001583,SO:0001578

proteinSubstitution

Protein substitution scores include SIFT and PolyPhen. You can query using the score {protein_score}[<|>|<=|>=]{number} or the description {protein_score}[~=|=]{description}

polyphen>0.1,sift=tolerant

conservation

Filter by conservation score: {conservation_score}[<|>|<=|>=]{number}

phastCons>0.5,phylop<0.1,gerp>0.1

populationFrequencyAlt

Alternate Population Frequency: {study}:{population}[<|>|<=|>=]{number}.

1kG_phase3:ALL<0.01

populationFrequencyRef

Reference Population Frequency: {study}:{population}[<|>|<=|>=]{number}.

1kG_phase3:ALL<0.01

populationFrequencyMaf

Population minor allele frequency: {study}:{population}[<|>|<=|>=]{number}.

1kG_phase3:ALL<0.01

transcriptFlag

List of transcript annotation flags.

When used together with gene, biotype or ct, all filters will need to match within the same transcript.

CCDS, basic, cds_end_NF, mRNA_end_NF, cds_start_NF, mRNA_start_NF, seleno

geneTraitId

List of gene trait association id.

umls:C0007222

OMIM:269600

trait

transcriptFlagList of traits, based on ClinVar, HPO, COSMIC, i.e.: IDs, histologies, descriptions,...

 

clinicalSignificance

Clinical significance: benign, likely_benign, likely_pathogenic, pathogenic

 

go

List of GO (Gene Ontology) terms.

GO:0002020

expression

List of tissues of interest.

lung

proteinKeyword

List of Uniprot protein variant annotation keywords

 

drug

List of drug names

 

functionalScore

Functional score: {functional_score}[<|>|<=|>=]{number}

cadd_scaled>5.2 , cadd_raw<=0.3

customAnnotation

Custom annotation: {key}[<|>|<=|>=]{number} or {key}[~=|=]{text}

 

annotationExists

Return only annotated variants

 


Parameter combination

When using together two or more filters of gene, ct, biotype or transcriptFlag, all filters will need to match within the same transcript. [#1214]

Query Options

Modifies over the variants to return.

KeyDescriptionExample
limitNumber of elements to return.100
skipNumber of elements to skip.100
sortSort variants by positiontrue
include

Fields from the Variant's model to be included in the response

See Variant Fields.

chromosome,start,reference,alternate
exclude

Fields from the Variant's model to be excluded in the response.

Ignored if "include" is present.

See Variant Fields.

studies.stats,annotation.expression
summary

Selects an small amount of fields to return.

Ignored if "include" or "exclude" are present.

See Variant Fields.

true
includeFormat

List of FORMAT names from Samples Data to include in the output.

Accepts "all" and "none".

AD,DP
includeGenotype

Include genotypes, apart of other formats defined with include

If "GT" is not provided in "includeFormat" or this parameter is false, genotypes won't be returned.

true
includeStudy

List of studies to be included in the result.

Accepts "all" and "none".


includeFile

List of files to be included in the result.

Accepts "all" and "none".


includeSample

List of samples to be included in the result.

Accepts "all" and "none".


unknownGenotypeReturned genotype for unknown genotypes. Common values: [0/0, 0|0, ./.]
sampleLimitLimit the number of samples to be included in the result
sampleSkipSkip some samples from the result. Useful for sample pagination.
sampleMetadataReturn the samples metadata group by study. Sample names will appear in the same order as their corresponding genotypes.

Variant Fields

The parameters include and exclude accepts a list of Variant Fields. This is a list with all the accepted values. Some short alias to those fields are listed in italic.

  • id
  • chromosome
  • start
  • end
  • reference
  • alternate
  • length
  • type
  • studies
    • studies.samplesData | samples | samplesData

    • studies.files | files

    • studies.stats | stats

    • studies.secondaryAlternates

    • studies.studyId

  • annotation
    • annotation.ancestralAllele
    • annotation.id
    • annotation.xrefs
    • annotation.hgvs
    • annotation.displayConsequenceType
    • annotation.consequenceTypes
    • annotation.populationFrequencies
    • annotation.minorAllele
    • annotation.minocohortStatsRefrAlleleFreq
    • annotation.conservation
    • annotation.geneExpression
    • annotation.geneTraitAssociation
    • annotation.geneDrugInteraction
    • annotation.variantTraitAssociation
    • annotation.functionalScore
    • annotation.additionalAttributes

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