An updated set of files showing the 1000 Genomes phase three variation calls on GRCh38 is now available. These files are based on dbSNP 149 and a “liftover” mapping from the GRCh37 genome assembly used by the 1000 Genomes Project to the newer GRCh38 assembly. In lifting over, equivalent regions of the two assemblies are identifed, enabling coordinates in one assembly to be mapped to the other. The liftover was done by dbSNP, with additional work contributed by EGA and EVA. As the files contain data from dbSNP, structural variants (those greater than 50bp in length) are not present in these files but can be accessed via Ensembl.
The files are available on our FTP site.
If you have questions about these files, please contact us at info@1000genomes.org.