From jillmrubens.its.unimelb.edu.au  Mon Nov  7 20:18:42 2011
From: Jill Maddox <jillmrubens.its.unimelb.edu.au>
To: Multiple Recipients of <crimap-usersanimalgenome.org>
Subject: Re: crimap
Date: Mon, 07 Nov 2011 20:18:42 -0600

Hi Anna

As Zhiliang says if you want to correspond with Phil Green (Genome Sciences
Department, Washington University,
http://www.gs.washington.edu/faculty/green.htm) then you need to e-mail him
directly and you will be incredibly lucky if he replies - he hasn't replied
to any of my e-mails about CRI-MAP.

In my experience when a gen file is correctly specified (no extra
characters or missing genotypes) CRI-MAP sometimes misses noninheritances
but it doesn't give false noninheritances. The missing inheritances bug has
been fixed in the next version of CRI-MAP that we are currently developing.
So it is possible that there is a problem in your gen file. One way of
checking that a gen file is OK is to unmerge the last locus from it (using
the unmerge program - I've attached a version of unmerged that was updated
by Ian Evans) and check that the resulting gen file is OK. If the gen file
for this marker is incorrect then there is a problem with the gen file.

Regards

 
Jill 
At 06:05 AM 5/11/2011, Anna Puig wrote: 

>
>Dear Green, 
> 
>I am using crimap_2.503a_inc_doc.tar.gz in unix. When running my .gen file, 
>having 235 SNP markers, with the prepare option I found that there were a 
>lot of non-inheritances. Though, we checked the mendelian inheritance 
>through pedstats program and it did not detect any error so it run 
>perfectly. In addition we have test it with only a part of the pedigree and 
>it works well. Nevertheless when adding all animals in .gen file it 
>detected the non-inheritance error for hardly all animals. Then when fixed 
>option was run I found a large cM map not corresponding with the real 
>physical map. I wondered how does it detect inheritances and if 340 animals 
>is too large in this case. 
> 
>Thank you, 
> 
>Anna 
> 
> 

 
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Jill Maddox 16 Park Square Port Melbourne, 3207 Australia phone: 03 9646
0428 E-mail: jillmrubens.its.unimelb.edu.au

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