Live Demo - Dnaerys

1000 Genomes Project Dataset

1000 Genomes 30x on GRCh38 dataset sequenced & aligned by New York Genome Center is available for querying:

Web UI: db.dnaerys.org:443
gRPC: db.dnaerys.org:7443
REST: db.dnaerys.org:8443

Dataset contains 3202 samples with 130 552 684 unique variants: 2504 unrelated samples from the phase three panel and additional 698 samples, related to samples in the 2504 panel (1598 males, 1604 females total; see references).

Dataset is VEP & ClinVar annotated.

Note

db.dnaerys.org server is located Down Under, hence consider round trip times

Web UI

Web interface for ad-hoc exploration: https://db.dnaerys.org

Note

Web client is using REST API and should not be used for performance evaluation. gRPC-Web based version is coming soon.

gRPC

examples below use gRPCurl as a client
- any gRPC client should work in principle
API declarations have to be provided to a client
- examples below use declarations from gRPC API which are stored in dnaerys.proto

Beacon

a variant in TP53

grpcurl \
  -proto dnaerys.proto \
  -d '{"chr":"17", "pos":"7662034", "alt":"A", "assembly":"GRCh38"}' \
  db.dnaerys.org:7443 \
  org.dnaerys.cluster.grpc.DnaerysService/Beacon

by coordinates

homozygous & heterozygous variants from TP53 from all samples, limiting response by 10 variants

grpcurl \
  -proto dnaerys.proto \
  -d '{"chr":"17", "start":"7661779", "end":"7687546", "hom":"true", "het":"true", "limit":"10", "assembly":"GRCh38"}' \
  db.dnaerys.org:7443 \
  org.dnaerys.cluster.grpc.DnaerysService/SelectVariantsInRegion

by annotations

MISSENSE SNVs in transcripts with high impact and PATHOGENIC ClinVar annotations in TP53, both homozygous & heterozygous

grpcurl \
  -proto dnaerys.proto \
  -d '{"chr":"17", "start":"7661779", "end":"7687546", "hom":"true", "het":"true", "limit":"10", "ann": {"vtypes":"SNV", "ftypes":["TRANSCRIPT"], "impact":["HIGH"], "consequences":"MISSENSE_VARIANT", "clnsgn":"PATHOGENIC"}, "assembly":"GRCh38"}' \
  db.dnaerys.org:7443 \
  org.dnaerys.cluster.grpc.DnaerysService/SelectVariantsInRegion

Pathogenic homozygous variants in sample (HG00447) in BRCA2

grpcurl \
  -proto dnaerys.proto \
  -d '{"chr":"13", "start":"32315086", "end":"32400268", "hom":"true", "samples":"HG00447", "ann": {"clnsgn":["PATHOGENIC"]}, "assembly":"GRCh38"}' \
  db.dnaerys.org:7443 \
  org.dnaerys.cluster.grpc.DnaerysService/SelectVariantsInRegionInVirtualCohort

selecting samples

Select all samples with pathogenic homozygous variants in transcripts in TP53

grpcurl \
  -proto dnaerys.proto \
  -d '{"chr":"17", "start":"7661779", "end":"7687546", "hom":"true", "ann": {"ftypes":["TRANSCRIPT"], "clnsgn":["PATHOGENIC"]}, "assembly":"GRCh38"}' \
  db.dnaerys.org:7443 \
  org.dnaerys.cluster.grpc.DnaerysService/SelectSamplesInRegion

kinship

Return kinship coefficients φ for all possible pairs in samples HG00418, HG00419, HG00420 (related trio)

grpcurl \
  -proto dnaerys.proto \
  -d '{"samples": ["HG00418", "HG00419", "HG00420"]}' \
  db.dnaerys.org:7443 \
  org.dnaerys.cluster.grpc.DnaerysService/Kinship

by inheritance models

De Novo

grpcurl \
  -proto dnaerys.proto \
  -d '{"parent1":"HG00418", "parent2":"HG00419", "proband":"HG00420", "limit":"1" }' \
  db.dnaerys.org:7443 \
  org.dnaerys.cluster.grpc.DnaerysService/SelectDeNovo

Homozygous Recessive

grpcurl \
  -proto dnaerys.proto \
  -d '{"unaffected_parent1":"HG00418", "unaffected_parent2":"HG00419", "affected_child":"HG00420", "limit":"1" }' \
  db.dnaerys.org:7443 \
  org.dnaerys.cluster.grpc.DnaerysService/SelectHomRecessive

Heterozygous Dominant

grpcurl \
  -proto dnaerys.proto \
  -d '{"affected_parent":"HG00418", "unaffected_parent":"HG00419", "affected_child":"HG00420", "limit":"1" }' \
  db.dnaerys.org:7443 \
  org.dnaerys.cluster.grpc.DnaerysService/SelectHetDominant

REST

Dnaerys does not provide REST API

when gRPC can not be used (e.g. for web browsers applications), a gateway can be used as an API Gateway proxy
- Variant Store Abstraction Layer instance is used as a proxy in examples below
REST API shall not be used for any DBMS performance evaluation - requests are significantly slowed down by marshalling & unmarshalling between the 2 protocols in VSAL
selecting by annotations is not supported by VSAL atm
jq in commands below is optional

GA4GH Beacon

VSAL provides GA4GH Beacon v0.2 API
- NB: Beacon v0.2 coordinates are 0-based, as opposed to Dnaerys/VSAL/VCF coordinates, which are 1-based
GA4GH Beacon v2 API is coming soon

curl "https://db.dnaerys.org:8443/vsal/beacon-v0dot2/query?chrom=17&pos=7662033&allele=A&ref=hg38" | jq

by coordinates

select 10 homozygous variants from TP53 from all samples

curl "https://db.dnaerys.org:8443/vsal/core/find?dataset=1000GP&chromosome=17&positionStart=7661779&positionEnd=7687546&hom=true&het=true&limit=10&asm=hg38" | jq

in samples

select homozygous variants in sample (HG00447) in BRCA2, limiting response by 10 variants

curl "https://db.dnaerys.org:8443/vsal/core/find?dataset=1000GP&chromosome=13&positionStart=32315086&positionEnd=32400268&hom=true&limit=10&asm=hg38&samples=HG00447" | jq

select heterozygous variants in sample (HG00447) in BRCA2, limiting response by 10 variants

curl "https://db.dnaerys.org:8443/vsal/core/find?dataset=1000GP&chromosome=13&positionStart=32315086&positionEnd=32400268&het=true&limit=10&asm=hg38&samples=HG00447" | jq

selecting samples

select all samples with homozygous variants in TP53

curl "https://db.dnaerys.org:8443/vsal/core/find?dataset=1000GP&chromosome=17&positionStart=7661779&positionEnd=7687546&hom=true&selectSamplesByGT=true&asm=hg38" | jq