Supported Formats

VarLens supports several JSON-based data formats for variant import.

JSON Columnar Format

The most common format. Data is organized with a header array describing columns and a data array of row values. Files must be gzip-compressed (.json.gz).

{
  "CaseName": {
    "header": [
      { "id": "Chr", "type": "text", "label": "Chromosome" },
      { "id": "Pos", "type": "number", "label": "Position" },
      { "id": "Ref", "type": "text", "label": "Reference" },
      { "id": "Alt", "type": "text", "label": "Alternate" },
      { "id": "Gene", "type": "dictionary", "label": "Gene",
        "dataDictionary": { "1": "BRCA1", "2": "TP53" } },
      { "id": "Consequence", "type": "dictionary", "label": "Consequence",
        "dataDictionary": { "1": "HIGH", "2": "MODERATE" } }
    ],
    "data": [
      ["1", 100000, "A", "G", "1", "2"],
      ["17", 200000, "C", "T", "2", "1"]
    ]
  }
}

Header Types

• text — Plain text value
• number — Numeric value
• dictionary — Lookup value referencing a dictionary map in the header

Recognized Column IDs

Column ID	Maps to	Notes
Chr	Chromosome
Pos	Position
Ref	Reference allele
Alt	Alternate allele
Gene	Gene symbol	Dictionary type
Consequence / Impact	Consequence severity	Dictionary: 1=HIGH, 2=MODERATE, 3=LOW, 4=MODIFIER
Func / VarType	Functional class
selectedTranscript	Transcript	Dictionary type
cDNA / HGVS_C	cDNA change
AAChange / HGVS_P	Protein change
GnomadAF / GnomTotal	gnomAD AF
CADDPhredScore	CADD score
Qual-Index / Qual	Quality score
ClinVSig / ClinVar	ClinVar significance
GTNum-Index / Genotype	Genotype
HpoSimScore	HPO similarity	Dictionary type
MoI	Mode of inheritance	Dictionary: AD, AR, XLD, etc.
Omim	OMIM number

JSON Object Format

Structured format with metadata and sample-level variant objects:

{
  "metadata": { "version": "1.0" },
  "samples": {
    "SampleA": {
      "variants": [
        {
          "chr": "1",
          "pos": 100000,
          "ref": "A",
          "alt": "G",
          "gene_symbol": "GENE1"
        }
      ]
    }
  }
}

JSON Simple Format

A flat array of variant objects:

{
  "variants": [
    {
      "chr": "1",
      "pos": 100000,
      "ref": "A",
      "alt": "G"
    }
  ]
}

Compression

All JSON formats must be gzip-compressed (.json.gz). Uncompressed .json files are not currently supported.