I just wanted to thank everyone who has sent me additional
information. The FAQ continues to improve at a remarkable
rate. The May28 release will be of significant utility to
researchers.
Steve Lincoln has signed on as a co-editor/co-author. His
experience/expertise in linkage analysis will complement
some of my weaknesses in the more theoretical aspects of this
subject. Welcome aboard Steve!
The FAQ is now available via anonymous ftp from:
ursula.ee.pdx.edu in /pub/users/cat/rootd
sellwood.ohsu.edu in /pub/linkagefaq
I'm updating those copies every couple days, but those are
not "release" versions. They're primairly so that, if you
want to contribute something, you don't repeat what is already
accomplished.
Please send information in any related topic, but there are
several areas where I would like to specifically solicit
information:
1) crimap
I do not have an ftp site for crimap. I do have the
multimap/lispcri site in Pittsburgh. Is crimap
available anywhere via anon-ftp? What about the
"crimap utilities" package (PIC/HET, twotable, faminfo,
genlink, linkgen, preinput, unmerge, unmerge2)? I'm not
interested in setting up a large anon-ftp site, but I would
really like having these programs available somewhere.
2) internet resources
Finding stuff on the internet is a real pain/timewaster.
Please continue to send me ftp, gopher, and www sites with
useful linkage information. A paragraph briefly describing
what is there is also useful. Check the FAQ to see what
I already have.
3) file formats
The following are file-formats that I have identified:
crimap(.gen), linkage, peddraw(mac), ped.out, liped,
simlink (I've probably forgotten several...). I've
written some perl scripts to convert between a couple of
them. Many other people have written programs to convert
between them. We keep on reinventing the wheel. I want to
collect a complete set of programs/scripts which, once and
for all, convert between these different formats. Please
email me source code (preferably in perl, c, sed, or awk).
If we can put together this collection, we all benefit.
I'm particulairly interested in finding source for
Santosh Mishra's mkcrigen program (which converts from
ped.out to .gen format) I only have a sparc2 executable
and its an old version which can only handle 80 markers.
Santosh Mishra said that he modified it to handle 500 markers,
but he's disappeared, the code's disappeared, and we're
constantly merging 80-marker .gen files...:-(
4) .gen file comparison programs
I've written a couple perl programs which compare .gen
files--but they're not that great. I've also had a
request for a program which compares different markers
in the same .gen file. If you send me source, I'll
pick the best and make certain it becomes available-
(with the ftp site listed in the FAQ).
That's all I can think of for now. Email submissions
to rootd at ohsu.edu If we work together, we can stop
searching/reinventing stuff and get on with our
research.
Thanks again for all the support!
Darrell Root
rootd at ohsu.edu
