NAME
origins - infer the grandparental origins of marker alleles in a set of CEPH pedigrees.
SYNOPSIS
origins [options]
DESCRIPTION
origins is a preprocessor for Meiotic Breakpoint Environment programs. origins reads in a pedigree description file and an allele description file in a format which is a subset of the file format for the linkage program. If no command line options are specified, it reads the files pedin.dat and datain.dat, and produces a formatted report on standard output.
OPTIONS
The following options may be used to control the files read by origins, and the reports produced. GNU style long options may also be used in place of the short options. Long options must be separated from their arguments with an ``='', and may not have spaces separating the option from the argument.
PEDIGREE FILE
The pedigree information file contains one line for each member of each pedigree. Each line contains the following information. pedigree number, id number, father's id, mother's id, first offspring id, next paternal sibling id, next maternal sibling id, sex, an unused field for the "proband status", followed by the marker data for each locus in the datain file. By convention, the father and mother of the third generation are ID 1 and 2 respectively.
1 1 0 0 3 0 0 1 1 1 2 2 3 1 4 1 2 0 0 3 0 0 2 0 1 1 1 2 2 3 1 3 1 2 0 4 4 1 0 2 1 3 2 1 3 1 4 1 2 0 0 0 2 0 1 1 2 2 2 4LOCI FILE
3 0 0 5 0 0.0 0.0 0 1 2 3 3 2 # NAME1 0.5 0.5 3 3 # NAME2 0.33 0.33 0.34 3 4 # NAME3 0.25 0.25 0.25 0.25MAP ORDER FILE
41 3 10This file shows the linear map of the 3 markers which are 41st, 3rd, and 10th in the datain.dat file.
BUGS
origins does not currently support binary coded (type 2) alleles in the allele description file, although linkage(1) does.
SEE ALSO
linkage(1)
AUTHOR
Humberto Ortiz Zuazaga,
University of Puerto Rico
Internet address humberto -at- hpcf.upr.edu.
Rosemarie Plaetke,
University of Alaska at Fairbanks
Internet address ffrp -at- uaf.edu.
Most recent change: 2007/9/3 at 22:24
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