Haplo

Haplotyping with computation of conditional probabilities

Version: 1.00

Last Update: 5 Feb 1996

Authors: Daniel E. Weeks and Kenneth Lange

Copyright: (c) 1996 Daniel E. Weeks

Collaborators: Jeffrey R O'Connell and Eric Sobel

Language: Fortran 77 (ANSI standard)

Distribution: As part of the Programs for Pedigree Analysis

Documentation: In the Programs for Pedigree Analysis documentation

Files: The source files are only available as part of the Programs for Pedigree Analysis distributed by Kenneth Lange (klange@umich.edu).

Running: The locus and pedigree files must be in MENDEL-format. If your data are in LINKAGE-format, run LinkMend to convert them to MENDEL-format. The default names for the locus and pedigree files are 'locus.dat' and 'pedm.dat'.

Frequently Modified Options:

You generally have to modify the following options:

• If your locus file has another name, choose option 2 : [ 2 LOCUS FILE locus.dat]
• If your pedigree file has another name, choose option 3 : [3 PEDIGREE FILE pedm.dat]
• The EXTRA array contains the recombination fractions along your map. You should choose option 8 and enter them. These recombination fractions are echoed back to the output file 'haplo.dat'. [8 EXTRA CONSTANTS FOR PROBLEM 0. 0. 0. 0. 0.]
• Choose option 9 to input the names of the loci for this problem. These names must match those given in locus.dat. [9 NAMES OF LOCI IN PROBLEM]
• Use option 17 to set the number of parameters to one less than the number of loci. That is, the number of parameters is equal to the number of recombination fractions [17 NUMBER OF PARAMETERS 1]
• Once you are ready to run, choose option 21: [21 ACCEPT PROBLEM]

 

Input files:

• locus.dat: locus file in MENDEL-format
• pedm.dat : pedigree file in MENDEL-format
• batch.dat: batch file (if run non-interactively).

The batch file must contain at least the marke rnames (menu option #9), the intermarker recombination fractions (menu option #8), and the number of recombination fractions (menu option#17). The intermarker recombination fractions should be given in order as entries in the EXTRA array (menu option #8).

Output files:

• haplo.sum: Listing of the most likely haplotypes, along with
• their conditional probabilities.
• haplo.ped: List of all the haplotypes, with their conditional probabilities. This list may be sorted by the extra program 'hapsort'.
• haplo.dat: standard MENDEL output

 

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Additional program:

HAPSORT

HAPSORT takes the haplo.ped output file and sorts the haplotypes by probability, placing the sorted output in haplo.sort, and a listing of the most probable haplotype for each individual in haplo.best.

 

Input files:

• haplo.ped

 

Output files:

• haplo.sort
• haplo.best

 

Source Files:

• hapsort.f
• indexx.f <= FORTRAN program from Numerical Recipes

 

NOTE: We do not distribute indexx.f.

Compiling:

f77 -o hapsort hapsort.f indexx.f

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If you have any questions or comments contact dweeks@pitt.edu