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From listmasteranimalgenome.org  Mon Nov 21 17:06:42 2022
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From: "Gwenola Tosser" <gwenola.tosserinrae.fr>
Postmaster: submission approved by list moderator
To: Members of AnGenMap <angenmapanimalgenome.org>
Subject: collecting SNPs for updates of the sheep/goat chips
Date: Mon, 21 Nov 2022 17:06:42 -0600

Dear colleague(s),

We are collecting SNPs for the next update(s) of the (sheep and goat)
chip(s).

The deadline for submission of Goat SNPs to be included in the update of
Goat_IGGC_65K_v2 Illumina chip is November the 25th (10 to 12 K additional
SNPs allowed).

Please submit your SNPs here: http://image.sigenae.org/

The current strategy for the update is to start from the current chip
content
https://www.goatgenome.org/...016_A2.csv
and:
- Remove 760 monomorphic GBS SNPs > replace them
- Remove useless PRP variants
- Add SNPs in candidate genes
  o SHBG/TMEM154/orthology with paratuberculosis region in cattle
  o casein cluster and ~1MB away
- Add SNPs collected through the web interface
- Add LOF mutations from VarGoats dataset
- Add Low MAF SNPs
- Add 1K ancestral SNPs from IMAGE chip

Any suggestion/comment/question is welcome.

Regards
Gwenola Tosser-Klopp

PS : Apologies for double posting

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please send an e-mail to gwenola.tosserinrae.fr with unsubscribe
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Gwenola Tosser-Klopp, PhD, HDR
INRAE-GenPhySE-Génétique, Physiologie et Systèmes d'Elevage-UMR1388
Equipe GenROC-Génomique des Ruminants Ovins et Caprins
Bureau C212a
24 Chemin de Borde Rouge - Auzeville
CS 52627
31326 Castanet Tolosan cedex
FRANCE
(33)5 61 28 51 14

Je n’attends pas de vous une réponse en dehors de vos horaires de travail /
Responses to emails from me are only expected during your working hours

http://genphyse.toulouse.inra.fr/groups/genroc

Coordination of IGGC and VarGoats:
http://www.goatgenome.org/


 
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