origins(1) manual page

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origins - infer the grandparental origins of marker alleles in a set of CEPH pedigrees.


origins [options]


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.


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.

-h [ --help ]
Prints a brief help message on standard output.

-p file [ --pedin=file ]
Specifies the name of the pedigree description file. If this option is not present, the program will read the file pedin.dat by default.

-d file [ --datain=file ]
Specifies the name of the loci description file. If this option is not present, the program will read the file datain.dat by default.

-a file [ --anain=file ]
Specifies the name of a file containing the ID numbers of markers forming a linear map. The ID numbers are derived from the order of the markers in the datain file. These markers will be printed first, in the order they are found in the anain file. If no file is specified, the markers will be printed in the order they appear in the datain file instead.

-l file [ --labels=file ]
Specifies the name of the file to which a listing of inferred grandparental labelings should go. This listing is not produced if the option is absent. This file may be used as input to the bpa program.

-r file [ --report=file ]
Specifies the name of the file to which the formatted report should go. The default is to send the report to standard output.


Need pedigree, allele, report, and labeling samples.

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 4
The loci description file contains a header, followed by the descriptions of each locus. The first line in each locus description must have a comment of the form `` # {name}''. The first word after the ``#'' is used to identify the locus in reports.

 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 0.25
The anain file contains one marker ID per line, listed in the order they should appear in the genetic map.

This file shows the linear map of the 3 markers which are 41st, 3rd, and 10th in the datain.dat file.


origins does not currently support binary coded (type 2) alleles in the allele description file, although linkage(1) does.




Humberto Ortiz Zuazaga, University of Puerto Rico Internet address humberto -at- Rosemarie Plaetke, University of Alaska at Fairbanks Internet address ffrp -at-

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Troglodita approved!

Humberto Ortiz Zuazaga

Most recent change: 2007/9/3 at 22:24
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