1)You will need some initial linkage data. Here's an examplefile for testing.
Its referred to as ex1.pre in the following documents:
ex1 father 0 0 1 2 1 2
ex1 mother 0 0 2 1 1 1
ex1 dau1 father mother 2 1 1 2
ex1 dau2 father mother 2 2 1 2
ex1 son1 father mother 1 2 1 2
ex1 dau3 father mother 2 1 1 1
ex1 son2 father mother 1 1 1 1
Any text editor can be used to create a "pre" file.
2)"makeped" converts this pre file to a "ped" file. (eg ex1.ped)
The makeped program allows extensive editing of the file
to select a host of options including which analysis programs
will be used.
3)"preplink" creates a datafile. (eg ex1.dat)
The UNIX "cp" (aka copy) command copies the ped file
to pedfile.dat
eg
cp ex1.ped pedfile.dat
Then cp again
cp ex1.dat datafile.dat
4) pedfile.dat and datafile.dat are generic names for input files
for the LINKAGE and FASTLINK programs.
6)The FASTLINK programs "unknown" and "mlink" may now be executed.
The results are saved in a file called outfile.dat.
7) Telnet to one of the following machines
erg.musc.edu
photon.musc.edu
quark.musc.edu
janus.musc.edu
bcr.musc.edu
>If you cannot login, then send an e-mail to
postmaster@musc.edu
Request that your MUSC network account be upgraded
to allow you to have access to the BCR Resources
GCG programs.
8) Once logged in you will be in a c-shell UNIX environment.
ALL COMMANDS MUST BE TYPED in lower CASE!!!
Typing 'ls' will list all the files in your MUSC directory.
This MUSC directory is your "homeroom". You should be able
to list all your files with the 'ls' command.
9) If you have data in a particular sub-directory of your
homeroom, use the command 'cd dir-name' to change
your working directory.
10) Any appropriately formatted pedigree file can be converted
to an input file with the MAKEPED program.
type
makeped
to run the program -- you are prompted for an input filename and
output filename.
11) There is one GENEHUNTER program "gh".GENEHUNTER
reads the same input files as FASTLINK.
To run the programs simply type:
gh
This launches the program and enters you into a GENEHUNTER
environment( the UNIX prompt "%" will be replaced with
a "npl:x" prompt where x is an integer indicated the
number of executed commands thus far).
Typing a "?" gives you a nice menu of GENEHUNTER commands.
You must first type "load marker-locus-filename"
then "scan pedigree-filename". The Photo command is initiated
by typing "photo filename" where filename is what you want to call
the photo file. Postscript output may be started by typing
"postscript on"
There is an on-line help function requires that you add the following
line to your UNIX ".cshrc" file
setenv GH_DIR /usr/common/bcr/GENEHUNTER
12) There are 5 FASTLINK programs
Run UNKNOWN first then any of the following
ILINK,MLINK,LODSCORE,LINKMAP
The calling procedure is
unknown
mlink
or
unknown
lodscore
13) There is an "on-line" manual for these programs.
The complete series of "HOMOG" programs is listed below:
homog
homog1a
homog1b
homog2
homog3
homog4
homog3r
point4
mtest
Simply typing the program name should activate the respective
program.
eg
homog
should start the "homog" program.
The BCR at the Medical University of South Carolina
URL: http://bcr.musc.edu/
e-mail to Starr comments about this page.