broadinstitute / gnomad-browser

Explore gnomAD datasets on the web
https://gnomad.broadinstitute.org
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Pull specific variants for curators #986

Open phildarnowsky-broad opened 1 year ago

phildarnowsky-broad commented 1 year ago

Usually the curation team asks us for all variants on a set of genes. This time around, they have asked for a specific list of variants [attached]. In addition to the usual process, this requires some tweaks to the variant pull script.

variants_to_pull.csv

phildarnowsky-broad commented 1 year ago

Done. Pulled data is pasted below, since apparently you can't attach a JSON file to a comment.

phildarnowsky-broad commented 1 year ago
[
  {
    "reference_genome": "GRCh37",
    "variant_id": "1-1115954-C-T",
    "liftover_variant_id": null,
    "qc_filter": "PASS",
    "AC": 572,
    "AN": 188212,
    "n_homozygotes": 7,
    "annotations": [
      {
        "gene_id": "ENSG00000162571",
        "gene_symbol": "TTLL10",
        "transcript_id": "ENST00000379288",
        "consequence": "stop_gained",
        "loftee": "HC",
        "loftee_flags": null,
        "loftee_filter": null
      },
      {
        "gene_id": "ENSG00000162571",
        "gene_symbol": "TTLL10",
        "transcript_id": "ENST00000379289",
        "consequence": "stop_gained",
        "loftee": "HC",
        "loftee_flags": null,
        "loftee_filter": null
      },
      {
        "gene_id": "ENSG00000162571",
        "gene_symbol": "TTLL10",
        "transcript_id": "ENST00000379290",
        "consequence": "stop_gained",
        "loftee": "HC",
        "loftee_flags": null,
        "loftee_filter": null
      }
    ],
    "AF": 0.003039126091853867
  },
  {
    "reference_genome": "GRCh37",
    "variant_id": "1-1116222-C-CG",
    "liftover_variant_id": null,
    "qc_filter": "PASS",
    "AC": 448,
    "AN": 208820,
    "n_homozygotes": 1,
    "annotations": [
      {
        "gene_id": "ENSG00000162571",
        "gene_symbol": "TTLL10",
        "transcript_id": "ENST00000379288",
        "consequence": "frameshift_variant",
        "loftee": "HC",
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        "loftee_filter": null
      },
      {
        "gene_id": "ENSG00000162571",
        "gene_symbol": "TTLL10",
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        "consequence": "frameshift_variant",
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      },
      {
        "gene_id": "ENSG00000162571",
        "gene_symbol": "TTLL10",
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    "n_homozygotes": 7,
    "annotations": [
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        "gene_symbol": "C1orf168",
        "transcript_id": "ENST00000343433",
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        "transcript_id": "ENST00000343433",
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