<p>I have two genotype tables, one for parents generated from snp arrays following hg18 coordinates, and the other for their offspring generated from ngs following hg19 coordinates. I finished liftover from hg18 to hg19 for parental data (refer to <a href="https://www.biostars.org/p/93399/">this post</a>) and I got a new list of coordinates, but I found I couldn&#39;t merge the parental genotype with the new hg19 coordinates because I don&#39;t know how to pair the new coordinates with the old ones. I wonder if there is a way to get their matching relationship. Any idea? Thanks.</p>

<p>Thanks, Ashutosh. Problem solved. I changed the 4th column to unique IDs, eg 1.rs#, 2.rs#, 3.rs#. Then my worries are gone.</p>
