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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).

  2. When a filter accepts a list of values, they can be separated with:

    • Comma , : Which will define an OR operation between the separated elements
    • Semicolon ; : Which will define an AND operation between the separated elements

So, the query chromosome: 2,3 will return all variants with 2 and 3, but chromosome: 2;3 will return all variants in chromosomes 2 and 3, but chromosome: 2;3 will return an empty result, because there are no variants in chromosomes 2 and 3 at the same time.

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

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

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

sampleAnnotation

Selects some samples using metadata information from Catalog.

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

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

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

cohort

Select variants with calculated stats for the selected cohorts

 



Sample and Family Parameters

Parameter

Description

Example

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

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

Key

Parameter

Description

Format

Example

gene

List of genes, most gene IDs are accepted (HGNC, Ensembl gene, ...). This is an alias to 'xref' parameter

BRCA2,BMPR

panel

Filter by genes from the given disease panel

List of values. Accept negations.annotationExiststrue/falsectConsequence type SO term list.SO:0000045,SO:0000046xrefExternal referencesbiotypeList of biotypesproteinSubstitutionProtein substitution score


xref

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


biotype

List of biotypes,

protein_coding

ct

List of SO consequence types,

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

Conservation score. Phylop, phastCons or gerp.

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

phastCons>0.5,phylop<0.1,gerp>0.1

populationFrequencyAlt

Alternate Population Frequency

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

1000GENOMES

1kG_

phase_3

phase3:

AFR>0

ALL<0.

2

01

populationFrequencyRef

Reference Population Frequency

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

ESP

1kG_

6500

phase3:

AA<0

ALL<0.

2

01

populationFrequencyMaf

Population minor allele frequency

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

EXAC:AES>=0.6transcriptionFlags

1kG_phase3:ALL<0.01

transcriptFlag

List of transcript annotation flags.

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

geneTraitId

List of gene trait association

ids

id.

umls:C0007222

, List of gene

OMIM:269600

geneTraitName

trait

association namestrait

Cardiovascular Diseases

List of traits, based on ClinVar, HPO, COSMIC

hpoList of HPO terms.HP:0000545

, i.e.: IDs, histologies, descriptions,...

 

clinicalSignificance

Clinical significance: benign, likely_benign, likely_pathogenic, pathogenic

 

go

List of GO (

Genome

Gene Ontology) terms.

GO:0002020

,GO:0006508

expression

List of tissues of interest.

lung

proteinKeywords

proteinKeyword

List of Uniprot protein variant annotation keywords

 

drug

List of drug names

 

functionalScore

Functional score

, like cadd

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

cadd_scaled>5.2 , cadd_raw<=0.3

customAnnotation

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

 

annotationExists

Return only annotated variants

 


Query Options

Modifies over the variants to return.

KeyDescriptionFormatExample
limitNumber of elements to return.number100
skipNumber of elements to skip.number100
sortSort variants by positiontrue,falsetrue
include

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

See Variant Fields.

List of fieldschromosome,start,reference,alternate
exclude

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

Ignored if "include" is present.

See Variant Fields.

List of fields

type,studies.stats,annotation.geneDrugInteractionexpression
summary

Selects an small amount of fields to return.

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

See Variant Fields.

true,falsetrue
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

  • id
    Description:

-format.

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

true,false
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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