IUBio

preplink and makeped

T. Jeffrey Keen t.j.keen at leeds.ac.uk
Mon Mar 29 04:44:12 EST 1999


I think you are maybe overestimating, what Preplink can can actually do for you.

You have to provide descriptions of loci individually ie. locus type,
allele frequencies etc. 

Load your present linkage.dat file into Preplink via the option

(m) Read datafile

then

(k) See or modify loci description

then

(a) SEE OR MODIFY A LOCUS

You can then change the number and frequencies at this point
 
It's pretty intuitive after after you've made a few mistakes.

There's also a Web version (but I've never used it)

http://linkage.rockefeller.edu/gui/webpreplink.html

The best description of these programs is in the essential; Terwilliger
and Ott, "Handbook for Human Genetic Linkage,"

All this aside Cyrillic at: 

http://www.cherwell.com/cherwell/products/genetics/cyrillic/overview.htm 

will generate linkage.dat files and calculate allele frequencies automatically

In article <36FB6202.7362 at mipnet.fr>, calvas at mipnet.fr wrote:

> I use the lcp program with MLINK to do my linkage analysis.
> The first locus is the disease (2 alleles: affected or not) and the next
> ones are microsatellite markers.
> 
> Preplink does not seem to calculate the allele frequencies of each
> marker (according to the data I've entered with the makeped program ie
> family member, status, alleles for each marker...) and gives by default
> 2 alleles with 0.05 of frequency for each one (that's wrong!).
> 
> What do i have to do to to have the right allele frequencies calculated
> according to my results?
>




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