From huanimalgenome.org  Tue Oct  4 09:02:15 2016
Delivered-To: crimap-usersanimalgenome.org
From: "Littrell, John" <jlittrellmcw.edu> 
Postmaster: submission approved by list moderator
To: Multiple Recipients of Cri-Map Users <crimap-usersanimalgenome.org>
Subject: Marker selection
Date: Tue, 04 Oct 2016 09:02:15 -0500

Hi all,

Thank you for your help with my last questions. This time I have a question
about marker selection. We have more markers than we can fine map - 10,000 on
the smallest chromosome with only 600+ individuals in 60+ nuclear families. I
figured we would start with a reasonable number of markers and continue to
use more until build could no longer add more markers to the map (at the same
LOD) because there were not enough meioses. Well, we are now at 4000 markers
and the map continues to grow. It takes nearly two months to run. I need a
better strategy for the larger chromosomes.

I am looking for a way to select the most useful markers instead of a lot of
markers. Here are my questions: It is my understanding that using nuclear
families means that we have no phase information and as a result the order of
marker informativeness created by prepare is not useful. Is that correct?
There are several families in the pedigree that have grandparents
(unfortunately, usually for just one of the parents). Should we use those to
get an idea of informativeness or would that bias marker selection to those
families? Or would using MAF as an indicator of informativeness be a good
idea and the range of 0.25-0.50 reasonable?

Thank you for your help, again.

 
Jack 
Genetic map enthusiast