Class GeneDrop

java.lang.Object
  alun.util.Main
      GeneDrop

public class GeneDrop
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 GeneDrop input.par input.ped [ldmodelfile] [-a] > output.ped

where

• input.par is the input LINKAGE parameter file.
• input.ped is the input LINKAGE pedigree file.
• output.ped is the checked output LINKAGE pedigree file.
• 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

GeneDrop()

Method Summary

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

GeneDrop

public GeneDrop()

Method Detail

main

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