Class GeneDrops

java.lang.Object
  alun.util.Main
      GeneDrops

public class GeneDrops
extends Main

This program uses the multi locus gene drop method to simulate genotypes on a pedigree to match those in the input. That is, if an individual's genotype at a certain marker is observed -- that is not zero -- in the specified input file, an observation will be simulated and specified in the output file. The recombination fractions specified in the input parameter file are used so that the simulations on the ith locus are simulated properly conditional on the i-1th.

If a linkage disequilibrium model for the founder haplotypes is specfied this is used and the alleles frequencies in the input parameter file are ignored. An LD model file can be estimated from data using other programs such as HapGraph or IntervalLD .

Usage : java GeneDrops input.par input.ped n prefix [ldmodelfile] [-a]

where

• input.par is the input LINKAGE parameter file.
• input.ped is the input LINKAGE pedigree file.
• n is the number of simulations required.
• prefix is the prefix in the names of the output files. For example, if the prefix is "out" and n=5, the output will be in files called "out.1", "out.2", ... "out.5".
• ldmodelfile this is an optional argument specifiying a model for linkage disequilibrium between the loci to be used in simulating the founder alleles. If this is specified the allele frequency information in the parameter file is ignored.
• -a if this option is specified, simulated genotypes are output for all the individuals in the pedigree, not just the ones observed in the input.

Constructor Summary

GeneDrops()

Method Summary

static java.lang.String	format(int i, int p)
static void	main(java.lang.String[] args)

Methods inherited from class alun.util.Main

strip

Methods inherited from class java.lang.Object

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

Constructor Detail

GeneDrops

public GeneDrops()

Method Detail

main

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

format

public static java.lang.String format(int i,
                                      int p)