Liftover

We are curating using the hg38 genome assembly.

Older publications generally use the previous (hg19=hg37) assembly.

Several tools are available to convert ("lift over") coordinates from one assembly to another.

UCSC

The UCSC Liftover tool requires data to be entered as e BED (e.g. "chr4 100000 100001", 0-based) and position box ("chr4:100,001-100,001", 1-based).

For instance, these coordinates (hg19)

chrX:138612906-138612906

are converted to (hg38)

chrX:136923343-136923343

It us useful to compare the result with data from the original publication. Often, a "snippet" with surrounding code is available. For this example, the original variant is noted to be chrX:138612906A>G on hg19 (PMID: 24138812).

we have ACTTTCAC[A/G]ATC