json.md

JSON

json (VCF to JSON conversion)

Convert a VCF to JSON. This is most useful in the context of a web-service, where you can serve variant data for the purposes of visualization, browsing, etc. For an example of what this might look like, see the elegans variation variant browser.

The json command can be used to parse ANN columns (effect annotations) by specifying --annotation. Additionally, FORMAT fields (GT, DP, etc) can be zipped with sample names.

Usage:
  sc json [options] vcf region

Arguments:
  vcf              VCF to convert to JSON
  region           Region

Options:
  -i, --info=INFO            comma-delimited INFO fields; Use 'ALL' for everything
  -f, --format=FORMAT        comma-delimited FORMAT fields; Use 'ALL' for everything
  -s, --samples=SAMPLES      Set Samples (default: ALL)
  -p, --pretty               Prettify result
  -a, --array                Output as a JSON array instead of ind. JSON lines
  -z, --zip                  Zip sample names with FORMAT fields (e.g. {'sample1': 25, 'sample2': 34})
  -n, --annotation           Parse ANN Fields
  --pass                     Only output variants where FILTER=PASS
  --debug                    Debug
  -h, --help                 Show this help

Example

sc json --format=GT --zip --pretty tests/data/test.vcf.gz

Outputs:

{
  "CHROM": "I",
  "POS": 41947,
  "ID": ".",
  "REF": "A",
  "ALT": [
    "T"
  ],
  "QUAL": 999.0,
  "FILTER": [
    "PASS"
  ],
  "FORMAT": {
    "GT": {
      "AB1": [
        2,
        2
      ],
      "...": [
        0,
        0
      ]
    }
  }
}

You can also specify custom SGT and TGT output formats which transform GT fields from their typical output.

• GT - Outputs genotypes as [[0, 0], [0, 1], [1, 1], ...
• SGT - Outputs genotypes as 0/0, 0/1, 1/1, ...
• TGT - Outputs genotypes as T/T, A/T, A/A, ...