1000 Genomes Project Dataset

1000 Genomes 30x on GRCh38 dataset sequenced & aligned by New York Genome Center is available for querying via gRPC, gRPC-web & MCP protocols:

Dataset contains 3202 samples with 138 044 723 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). For details and attribution see references.

This dataset was annotated by:

Note

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

Model Context Protocol

OneKGPd - Model Context Protocol Server for 1000 Genomes Project Dataset. Our favorite style for asking genomes the questions!

gRPC

by coordinates

grpcurl \
  -proto dnaerys_1.17.2.proto \
  -d '{"chr":"17", "start":"7661779", "end":"7687546", "hom":"true", "het":"true", "limit":"10", "assembly":"GRCh38"}' \
  db.dnaerys.org:443 \
  org.dnaerys.cluster.grpc.DnaerysService/SelectVariantsInRegion

by annotations

grpcurl \
  -proto dnaerys_1.17.2.proto \
  -d '{"chr":"17", "start":"7661779", "end":"7687546", "hom":"true", "het":"true", "ann": {"clinsgn":"PATHOGENIC"}, "assembly":"GRCh38"}' \
  db.dnaerys.org:443 \
  org.dnaerys.cluster.grpc.DnaerysService/SelectVariantsInRegion

grpcurl \
  -proto dnaerys_1.17.2.proto \
  -d '{"chr":"17", "start":"7661779", "end":"7687546", "het":"true", "ann": {"feature_type":["TRANSCRIPT"], "impact":["HIGH"]}, "assembly":"GRCh38"}' \
  db.dnaerys.org:443 \
  org.dnaerys.cluster.grpc.DnaerysService/SelectVariantsInRegion

grpcurl \
  -proto dnaerys_1.17.2.proto \
  -d '{"chr":"17", "start":"7661779", "end":"7687546", "het":"true", "samples":"NA10842", "ann": {"clinsgn":["PATHOGENIC"]}, "assembly":"GRCh38"}' \
  db.dnaerys.org:443 \
  org.dnaerys.cluster.grpc.DnaerysService/SelectVariantsInRegionInSamples

selecting samples

grpcurl \
  -proto dnaerys_1.17.2.proto \
  -d '{"chr":"17", "start":"7661779", "end":"7687546", "het":"true", "ann": {"feature_type":"TRANSCRIPT", "clinsgn":"PATHOGENIC", "gnomad_exomes_af_lt":"0.0001"}, "assembly":"GRCh38"}' \
  db.dnaerys.org:443 \
  org.dnaerys.cluster.grpc.DnaerysService/SelectSamplesInRegion

by inheritance models

grpcurl \
  -proto dnaerys_1.17.2.proto \
  -d '{"parent1":"HG00418", "parent2":"HG00419", "proband":"HG00420", "chr":"1", "start":"1", "end":"248956422", "ann": {"am_class":"AM_LIKELY_PATHOGENIC"}}' \
  db.dnaerys.org:443 \
  org.dnaerys.cluster.grpc.DnaerysService/SelectDeNovo

grpcurl \
  -proto dnaerys_1.17.2.proto \
  -d '{"unaffected_parent1":"HG00418", "unaffected_parent2":"HG00419", "affected_child":"HG00420", "chr":"1", "start":"1", "end":"248956422", "ann": {"am_class":"AM_LIKELY_PATHOGENIC"}}' \
  db.dnaerys.org:443 \
  org.dnaerys.cluster.grpc.DnaerysService/SelectHomRecessive

grpcurl \
  -proto dnaerys_1.17.2.proto \
  -d '{"affected_parent":"HG00418", "unaffected_parent":"HG00419", "affected_child":"HG00420", "chr":"1", "start":"1", "end":"248956422", "ann": {"am_class":"AM_LIKELY_PATHOGENIC"}}' \
  db.dnaerys.org:443 \
  org.dnaerys.cluster.grpc.DnaerysService/SelectHetDominant

gRPC-web

gRPC-web proxy (Envoy) is available for web applications with full gRPC API:

1000 Genomes Project references

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