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 and LRG sequences (including transcript and protein sequences annotated on the RefSeqGene and LRG) or from RefSeqGene and 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