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From listmasteranimalgenome.org  Tue Jun 30 12:33:37 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 12:33:37 -0500

Paolo,

It's kind of you to have asked Illumina.

While correctly mapping data to new assemblies is vital for the utility
of chips as well as for information lift-over between the builds and data
curation/annotations moving forward, it's equally important for correct
match of SNP public ID (eg. 'rs' numbers) to Illumina IDs or any associated
SNP names.  Many of us suffer from time to time for missing such matches
in order to bring information together.

It would be nice if Illumina could kindly make such ID matches as "white
sheets" on all their products as public information (please correct me if
it's only me having a hard time to locate such data). It helps to promote
their products anyway.

Zhiliang


On Jun 30, 2020, at 11:17 AM, Paolo Zambonelli <paolo.zambonelliunibo.it> wrote:

Hello,

I recently asked Illumina to re-map all the SNPs of the 70k SNP chip to
version 11.1 of the porcine genome. They provided me an updated manifest
file. I don't know if I can share this file but I ask to Illumina technical
support, that is reading this message on cc, if it is possible. Otherwise
anyone that is interested can contact directly Illumina.

Best regards,

Paolo Zambonelli

Dr. Paolo Zambonelli, PhD
Researcher
DISTAL
Alma Mater Studiorum - Universit=E0 di Bologna
Viale G. Fanin, 46 - I-40127 Bologna - Italy
tel +39 051 20 88055
mobile +39 340 144 84 06
paolo.zambonelliunibo.it
skype paolo.zzz
https://www.unibo.it/...eb/paolo.zambonelli/
https://www.unibo.it/.../paolo.zambonelli/en


-----Messaggio originale-----
Da: Jrn Bennewitz [mailto:j.bennewitzuni-hohenheim.de]
Inviato: marted 30 giugno 2020 16.29
A: Members of AnGenMap
Oggetto: Sus scrofa genome - Illumina SNP chip

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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