How to convert plink data from 38th assembly to 37

Question

[eyb]

My goal is to downgrade plink(.bed, bim, fam) data from the 38th build to 37. What is the easiest way to do this?

I was reading liftOver documentation and I am confused. Because it only accepts its own .bed format to do the lifting. It looks like I can prepare such a file, from plink bim, but what with the rest plink files, bed, and fam? Are they not require any modification? Also if I were to create a liftOver bed file, I notice that there are two coordinates for each SNP:

chr1    743267  743268  rs3115860
chr1    766408  766409  rs12124819
chr1    773885  773886  rs17160939

And there is only one coordinate in the plink .map file, how do I convert my map file?

[desouzareis.r]

Hi,

There is a liftover library in python that you could use to liftover only a position like in

from pyliftover import LiftOver
lo = LiftOver('hg17', 'hg18')
lo.convert_coordinate('chr1', 1000000)

To convert the map file to bed you can add 1 for the second coordinate

Answer 1

[wenbinm]

I am having the same problem. This tool offers a good tutorial and a script to lift plink format data: https://genome.sph.umich.edu/wiki/LiftOver. We need to update both map and ped files. There is also a polished version: https://github.com/sritchie73/liftOverPlink/blob/master/README.md.

Another way is to first convert your plink data to vcf files using plink --recode. Then use GATK's LiftoverVcf tool to liftover vcf files.