FINAL DATA FORMATTING FOR LINKAGE PROGRAMS

At this point, your *.pre file should be error-checked and free of meiotic and formatting errors. And you should have created a pre-linkage file with any subset of pedigrees with the markers arranged in map order (accomplished by using the linkage pedigrees option of the program NEWPREP). The pre-linkage file output by newprep is now called a *.ped file. The next step is to convert your .ped file into a MAKEPED (.mk) file. Creating a .mk file will put your data into the proper format for recoding.

Step-by-step instructions are given below. The left side of the table contains the instructions and the right side (colored areas) represent what should show up on your screen. User input is in bold.

1. At the user prompt, type makeped *.ped *.mk, where * represents your file's specific prefix. Press (RETURN).	user@humgen%   makeped pedigree1.pre pedigree1.mk
1a. If, at the user prompt, you type only makeped (RETURN) the program will ask you for the file names.	user@humgen%   makeped
1b. The program will ask for the pedigree file. Type the name of your .ped file. Press (RETURN)	Pedigree file -> pedigree1.pre
1c. The program will ask for the name of the output file. Type in a file name for the output file. Press (RETURN)	Output file -> pedigree1.mk
2. The program will ask if there are any loops in the pedigree. Answer no. Press (RETURN). Loops refers to consanguinity loops. If any of your families have loops, you will need to break the loops after running MAKEPED then run MAKEPED again (see the LINKAGE manual).	Does your pedigree file contain any loops? (y/n) -> n
3. To have the program select probands automatically, answer yes. Press (RETURN)	Do you want probands selected automatically? (y/n) -> y
4. A new *.mk file should appear in your directory. (it should be named what you typed in STEP #1, or #1c). Look at the MAKEPED file by typing less and the name of your *.mk file at the user prompt. Press (RETURN). At the end of each row is the original pedigree and individual ID. Please note that MAKEPED renames individuals (and sometimes pedigrees), making it very difficult to compare post-MAKEPED data to original genotypes. For an explanation of what is in each column, see the LINKAGE manual. At right is how the example MAKEPED file appears.	user@humgen%   less pedigree1.mk 2 14 11 12 22 16 16 2 0 2 194 197 159 163 136 140 Ped: 2 Per: 2120 2 16 11 12 18 19 0 2 0 2 190 197 155 159 136 140 Ped: 2 Per: 2105 2 18 17 16 0 0 0 2 0 1 197 197 159 163 136 140 Ped: 2 Per: 2131 2 19 11 13 21 0 0 2 0 2 197 197 155 159 136 144 Ped: 2 Per: 2103 2 22 15 14 0 23 23 1 0 1 194 197 155 163 132 148 Ped: 2 Per: 2123 2 23 15 14 25 43 43 2 0 2 197 197 147 163 136 140 Ped: 2 Per: 2128 2 26 24 23 0 0 0 2 0 2 197 197 147 159 136 140 Ped: 2 Per: 2125

At this point you should have a *.mk file (processed through MAKEPED).

Now you can recode your data so that it can be analyzed. LINKAGE programs require that marker allele numbering start with 1 and increase +1 for the total number of alleles used in that file (for that marker), and RECODE will do that conversion for you, given a MAKEPED input file. The output is three files: the user-named and recoded MAKEPED file (.rec), and two files containing the allelic conversions (key.dat) and allele frequencies (recode.dat). You will use the recode.dat later to create the linkage parameter file, datain.dat.

RECODE was written by Dan Weeks, and does more than described here. His documentation is at /hg01/local/recode/readme. (To read it, type at your prompt: less /hg01/local/recode/readme.)

Please note that if you have several files to process through RECODE at once, you will need to either rename the key.dat and recode.dat files after each run, or create separate directories for the files, then run RECODE in each directory.

Step-by-step instructions are given below. The left side of the table contains the instructions and the right side (colored areas) represent what should show up on your screen. User input is in boldface.

1. At the user prompt, type recode. Press (RETURN)	user@humgen%   recode
2. The program will ask you if there is a disease locus. Type y for yes. Press (RETURN)	Is there a disease locus? (y/n)   y
3. Specify the number of liability classes. When the data have gone through newprep, enter the number of liability classes as 2 (to get it to register the fact that there is a liability column). If no liability column, enter 0. For more on liability classes, see the LINKAGE manual. Press (RETURN)	How many liability classes are there?   2
4. Specify the number of markers in your data. For the sample data pedigree1.mk, there are 3 markers. Press (RETURN)	How many marker loci are there?   3
5. Type the name of the .mk file you want recoded. In this example, it is pedigree1.mk.Press (RETURN)	What is the name of the input file?   pedigree1.mk
6. Specify what you want the recoded file to be called. In this example, the new file will be called pedigree1.rec. Press (RETURN)	What is the name of the recoded output file?   pedigree1.rec
7.After you complete STEP #6, the screen will fill up with columns of numbers. The example screen is shown at right.	2 1 0 0 11 0 0 1 0 2 2 9 10 14 0 0 1 0 2 3 0 0 14 0 0 2 0 2 4 0 0 19 0 0 2 0 2 5 11 12 22 16 16 2 0 2 6 0 0 22 0 0 1 0 2 7 11 12 18 19 0 2 0 Marker 1 has 4 alleles Marker 2 has 6 alleles Marker 3 has 5 alleles Writing out recoded data at 3 markers for (#) people to: pedigree1.rec The recoded pedigree file is: pedigree1.rec The allele key file is: key.dat Part of the datain.dat appears in: recode.dat

The recoded file should appear in your directory. (it should be named what you typed in STEP #6). An additional file called recode.dat should also be in your directory. The information in this file will be used to create your datain.dat file.