From John.Bastiaansen wur.nl Fri Mar 9 02:29:01 2012
From: "Bastiaansen, John" <John.Bastiaansenwur.nl>
Subject: RE: create Pedigree applying DATA and huge PEDIGREE files
To: Multiple Recipients of <angenmapanimalgenome.org>
Date: Fri, 09 Mar 2012 02:29:01 -0600
Dear Rohullah Abdullahpour,
The trimPed function in the R package pedigree is written to do exactly
what you describe. I runs in less than 1 minute on my laptop with a
simulated (random mating) pedigree file of 5 generations, 1 million animals
per generation, 100,000 animals with data in the last generation. The
resulting trimmed pedigree has 1.37 million records.
Best Wishes,
John Bastiaansen
Animal Breeding and Genomics Centre
Wageningen University
________________________________________
.From: Rohullah Abdullahpour [rohullah1979ayahoo.com]
.Sent: Friday, March 09, 2012 8:46 AM
.To: Multiple Recipients of <AnGenMapanimalgenome.org
.Subject: Re: create Pedigree applying DATA and huge PEDIGREE files
Dears,
The exact task that the original poster want to do, is extracting from a large
original pedigree a file which contains only animals who are relatives to
animals in data file, and non relatives removed, to save memory and time in
later analyses. This is done by finding parents of animals in data file then
finding parents of these parents and so on consecutively (i.e. tracing
generation by generation) until the animals in foundation population.
1) I think secateurs has no limitation in volume of pedigree file by itself!?
2) another way is Wombat (by Karin Meyer) which can do this and prune input
pedigree at the initial of any analysis and make a file (prunedpedfile1) (use
Linux 64 version and a simple model for analysis), then you can obtain the
pruned pedigree and use it for any purpose.
3) I wrote a program in visual Foxpro for my works but it needs time for
very large original pedigree.
Regards,
Rohullah Abdullahpour
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