Convert variant coordinates

Convert variant coordinates between different reference sequences.

There are several tools that allows users to project annotation data from one coordinate system to another.
These include:

NCBI Remap
  • Clinical remap allows for the remapping of features:
    • From assembly sequences to RefSeqGene (including transcript and protein sequences annotated on the RefSeqGene)
    • From assembly sequences to LRG (including transcript and protein sequences annotated on the LRG)
    • From RefSeqGene sequences to an assembly
    • From LRG sequences to an assembly

  • Assembly-Assembly allows the remapping of features from one assembly to another.

  • Alt loci remap allows for the mapping of features between the Primary assembly unit and the Alternate Loci and Patches assembly units available for GRC assemblies.
Ensembl - Assembly Converter

Maps coordinates between different reference genome assemblies

Mutalyzer

Provides a series of tools to check variant HGVS nomenclature and convert between different reference sequence systems.

VariantValidator

Enables accurate validation, mapping and formatting of sequence variants using HGVS nomenclature