#liftover

[pacm3n-blog1]

Updating SNP position on the chromosome, with liftOver et al

[pacm3n-blog1]

PLINK to the rescue(?)

LiftOver is a necesary step to bring all genetical analysis to the same reference build. LiftOver can have three use cases:

(1) Convert genome position from one genome assembly to another genome assembly

In most scenarios, we have known genome positions in NCBI build 36 (UCSC hg 18) and hope to lift them over to NCBI build 37 (UCSC hg19).

(2) Convert dbSNP rs number from one build to another

(3) Convert both genome position and dbSNP rs number over different versions

It is likely to see such type of data in Merlin/PLINK format.

We will explain the work flow for the above three cases. In the rest of this article, our example is to lift over from lower/older build to newer/higher build, as it is the common practice.

Using different tools, liftOver can be easy. For example, UCSC liftOver tool is able to lift BED format file between builds. With our customized scripts, we can also lift rsNumber and Merlin/PLINK data files.