by Gerrit van der Ende
Originally published August 8, 2014
As more is learned about the human genome, new Genome assemblies are released. For a given DNA sequence, coordinates are different between the Genome assemblies. In working with DNA to learn about genealogy, it is often necessary to convert DNA coordinates from one Genome assembly to another.
When you submit coordinates for SNPs to add to our catalog, you may submit one position but get a different position in confirmation. That’s because it’s a different build.
The following tutorial describes how to convert SNP coordinates between Genome assemblies.
The NCBI Genome Remapping Service at www.ncbi.nlm.nih.gov/genome/tools/remap can be used to carry out the conversion.
Example 1: Converting a coordinate from hg18 to hg19.
- On the website, in Genome Information, enter Homo sapiens for the source organism.
- In Source Assembly, “NCBI36 (hg18)” should be selected.
- In Target Assembly, “GRCh37 (hg19)” should be selected.
- In Data, Paste data here:, enter the sequence using the coordinates from the Source Assembly.
- The format ChrY:coordinate-coordinate should be used.
Example 2: Converting the position 20,000,000 in hg18 to its corresponding coordinate in hg19.
- ChrY:20000000-20000000 should be entered in the Paste Data Here: box. Click Submit.
- The Target Assembly coordinate is shown in the Mapping Report (sample) box, below Map Location. In this case, the Target Assembly (hg19) coordinate ChrY:21540612 is shown, meaning that hg18 20,000,000 has the corresponding hg19 coordinate of 21,540,612.
- To convert a sequence position from hg19 to hg18, “GRCh37 (hg19)” should be selected for the Source Assembly, and “NCBI36 (hg18)” should be selected for the Target Assembly. The hg19 coordinate should be entered in the Paste Data Here: box, and the hg18 coordinate will show below Map Location, in the Mapping Report (sample) box.