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

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: 

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

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

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

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

See Variant Fields.

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

Ignored if "include" is present.

See Variant Fields.

Selects an small amount of fields to return.

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

See Variant Fields.

List of studies to be included in the result.

Accepts "all" and "none".

List of files to be included in the result.

Accepts "all" and "none".

List of samples to be included in the result.

Accepts "all" and "none".