From listmaster animalgenome.org Tue Jun 30 12:30:57 2020
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From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
Subject: Re: Sus scrofa genome - Illumina SNP chip
Postmaster: submission approved by list moderator
To: Members of AnGenMap <angenmapanimalgenome.org>
Date: Tue, 30 Jun 2020 12:30:57 -0500
A short while ago the European Variation Archive (EVA) announced an
EVA Release which included successful transfer of 98.35% pig SNPs
as part of dbSNP transfer from NCBI. The mapping is on Sscrofa 11
build. (https://www.ebi.ac.uk/...view/GCA_000003025.6)
If your Illuminas SNPs are with 'rs' IDs and not include newer SNPs
that has not been submitted/processed by EVA, it would be relatively
straight forward to map your data.
Zhiliang
On Jun 30, 2020, at 09:28 AM, Jörn Bennewitz <j.bennewitzuni-hohenheim.de> wrote:
Recently we ordered Illuminas new GGP Porcine HD Array (70k).
Unfortunately SNP positions in the manifest file are based on Sus
scrofa genome version 10.2. Did anybody build a new map based on
version 11.1 and would like to share this information with us?
Sincerely, Jrn Bennewitz (University of Hohenheim, Germany)
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