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From listmasteranimalgenome.org  Tlistmaster May 27 17:25:04 2021
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From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
Postmaster: submission approved by list moderator
To: Members of AnGenMap <angenmapanimalgenome.org>
Subject: SNP mapping liftover from previous mapped genome assemblies to
       new builds
Date: Thu, 27 May 2021 17:25:04 -0500

Dear colleagues,

As part of our efforts to add abilities supporting all genome builds
within the Animal QTLdb for QTL and SNP association data mappings, we
developed a method, using bedtools and bwa software package, to have
successfully lifted SNPs from previously mapped Gallus_gallus-5.0 assembly
to the most recent chicken genome builds bGalGal1.mat.GRCg7b and
bGalGal1.pat.GRCg7w.  With a relatively long flanking sequence (160 bp)
fed to bwa, we were able to obtain a liftover rate as high as 95-97%.

We have deposited a copy of the build GRCg7b liftover results in the
NAGRP Data Repository (https://www.animalgenome.org/repository/chicken/
File: "Chicken_SNPliftover_toGRCg7b.vcf.gz") and welcome comments/tests.
As we will continue to exercise the process lifting SNPs from old to new
genome builds for cattle, pigs, sheep, and other species hosted in Animal
QTLdb, if you have similar needs for other species, we can also help.

Please let us know if making available of these liftover results is needed.
In addition, if there is a need for the pipeline/scripts, we can make them
available as well, perhaps via github.

Thanks for your attention,


Zhiliang
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