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Getting Started

Choosing an Endpoint

REST VariantValidator2 SHAIP provides multiple endpoints optimised for different types of input and analysis workflows. Selecting the correct endpoint is critical for both correctness and performance.

Use the following guidance:

Access

access

/shaip/VariantFormatter-v2

Use for:

  • Genomic HGVS descriptions
  • VCF lines and pseudo‑VCF inputs (chr-pos-ref-alt)
  • High-throughput processing pipelines

This is the recommended endpoint for most genomic inputs, providing fast mapping from genomic variants to transcript and protein representations.

/shaip/VariantValidator

Use for:

  • Full HGVS validation
  • Transcript-level HGVS (e.g. NM_...:c.)
  • Protein HGVS
  • Intronic variants and complex HGVS expressions
  • Validation of VCF and pseudo-VCF inputs when strict HGVS interpretation is required

This endpoint performs complete HGVS parsing, validation, correction, and mapping using the RefSeq transcript set.

/shaip/VariantValidator-ensembl

Use for:

  • All use cases supported by /VariantValidator
  • Workflows requiring Ensembl transcript definitions

This endpoint behaves identically to /VariantValidator but uses the Ensembl transcript set instead of RefSeq.

/shaip/tools/gene2transcripts-v2

Use for:

  • Resolving a gene into available transcripts
  • Identifying MANE or canonical transcript sets
  • Preparing transcript constraints prior to variant validation or formatting
  • Generating exon-level data (e.g. alignment spans, CIGAR strings) for downstream applications such as panel-based BED file generation

This endpoint is typically used as a preprocessing step before submitting variants to other endpoints.

/shaip/tools/hgvs2reference

Use for:

  • Retrieving the reference base or sequence for an HGVS description
  • Verifying reference alleles prior to variant processing
  • Supporting downstream sequence-level analyses

This endpoint returns reference data only and does not perform validation or consequence prediction.

Summary

  • Use variantformatter-v2 for speed and genomic inputs
  • Use variantvalidator for full HGVS validation (RefSeq)
  • Use variantvalidator-ensembl for Ensembl-based workflows
  • Use gene2transcripts-v2 to define transcript scope
  • Use hgvs2reference for reference sequence lookup only

Choosing the correct endpoint ensures accurate results, optimal performance, and appropriate handling of variant complexity.