Class MakeProbands

java.lang.Object
  MakeProbands

public class MakeProbands
extends java.lang.Object

This programs marks inividuals in a pedigree file as being or not being probands. It is designed to make Shags , SimShags , Hogs and SimHogs easier to use. The default action is to make each individual who has at least 10 genotypes called a proband, and all the others non-probands. This threshold can be changed with a command line argument. It is also possible to specify a file of individuals which will be made probands.

• Usage : java MakeProbands input.par input.ped [mincount]
• Usage : java MakeProbands input.par input.ped [probandfile]

where

• input.par is the input LINKAGE parameter file.
• input.ped is the input LINKAGE pedigree file.
• mincount this is an optional integer parameter specifying the minimum number of called genotypes that an idividuals must have to be made a proband.
• probandfile if the argument after the specified LINKAGE files cannot be read as an integer, it is assumed to be the name of a file specifying the probands. The file must contain one line for each proband and each line must have the kindred id number followed by the individual number.

Constructor Summary

MakeProbands()

Method Summary

static void

main(java.lang.String[] args)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MakeProbands

public MakeProbands()

Method Detail

main

public static void main(java.lang.String[] args)