/shaip/variantformatter-v2

Purpose

High-performance genomic → transcript → protein formatter.

Optimised for:

• Genomic HGVS
• VCF lines
• Pseudo-VCF inputs
• Batch processing

This endpoint is intended for high-throughput workflows where speed and controlled transcript mapping are required.

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Method

POST

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Path

/shaip/variantformatter-v2

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Input

Parameter	Type	Required	Description
variant_description	string or array	Yes	Variant input (HGVS, VCF, or pseudo-VCF). Multiple inputs via a JSON array or pipe delimited strings
genome_build	string	Yes	GRCh37, GRCh38, hg19, or hg38
transcript_model	string	Yes	refseq, ensembl, or all
select_transcripts	string or array	Yes	Transcript selection (see transcript_selection.md)
checkonly	boolean or "tx"	Yes	Validation mode
liftover_level	string or bool	No	Controls genomic liftover. True performs full liftover, primary excludes alternative scaffolds, and False disables liftover. Defaults to True.

---

Example

[
  {
    "variant_description": "17-50198002-C-A",
    "genome_build": "GRCh38",
    "transcript_model": "refseq",
    "select_transcripts": "mane_select",
    "checkonly": false,
    "liftover_level": false
  }
]

---

Example Response

{
  "17-50198002-C-A": {
    "errors": [],
    "flag": null,
    "17-50198002-C-A": {
      "p_vcf": "17-50198002-C-A",
      "g_hgvs": "NC_000017.11:g.50198002C>A",
      "selected_build": "GRCh38",
      "genomic_variant_error": null,
      "genomic_variant_warnings": null,
      "hgvs_t_and_p": {
        "NM_000088.4": {
          "t_hgvs": "NM_000088.4:c.589G>T",
          "p_hgvs_tlc": "NP_000079.2:p.(Gly197Cys)",
          "p_hgvs_slc": "NP_000079.2:p.(G197C)",
          "select_status": {
            "mane_select": true
          },
          "gene_info": {
            "symbol": "COL1A1",
            "hgnc_id": "HGNC:2197"
          },
          "transcript_version_warning": null,
          "gapped_alignment_warning": null,
          "gap_statement": null,
          "transcript_variant_error": null
        }
      }
    }
  },
  "metadata": {
    "variantvalidator_version": "4.0.0",
    "variantvalidator_hgvs_version": "4.0.0",
    "vvta_version": "vvta_2025_02",
    "vvseqrepo_db": "VV_SR_2025_02/master",
    "vvdb_version": "vvdb_2025_3",
    "variantformatter_version": "4.0.0"
  }
}

---

Behaviour

• Parses genomic and VCF-like variant inputs
• Performs genomic → transcript → protein mapping
• Applies transcript filtering based on select_transcripts
• Supports batch submission via arrays or pipe-delimited input
• Optionally performs genome build liftover when enabled

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Notes

• Multiple inputs
• "17-50198002-C-A|17-50197802-G-T" pipe delimited string
• '["17-50198002-C-A", "17-50198002-C-T"]'
• limit to 10 variants
• Fastest endpoint for genomic inputs
• Transcript selection behaviour is defined in transcript_selection.md
• Prefer mane_select, mane, or explicit transcript IDs for performance
• Avoid all and raw unless full transcript enumeration is required
• Disable liftover_level where not needed to maximise performance