Class CheckErrors

java.lang.Object
  alun.genapps.ObligatoryErrors
      alun.genapps.FindErrorProbs
          CheckErrors

Direct Known Subclasses:

GMCheck

public class CheckErrors
extends FindErrorProbs

This program finds the posterior probabilities of errors for genotypes on individuals in pedigrees given a set of observed genotypes and the pedigree structure.

Usage : java CheckErrors input.par input.ped [thresh1] [thresh2] [prior]

where

• input.par is a LINKAGE parameter file
• input.ped is a LINKAGE pedigree file
• thresh1 specifies the minimum value for the overall probability that there is at least one genotyping error at a particular locus above which errors are reported. The default is 50%.
• thresh2 specifies the minimum value for reporting individual error probabilities, given that the overall error probability exceeds thresh1 . The default is 25%.
• prior is the prior probability that any genotyping call is in error. The default is 1%.

This analyzes the data in the input files, locus by locus and kindred by kindred. It computes the posterior probability that each genotype call is in error using a standard graphical modeling forward-backward algorithm. It replaces the program GMCheck .

For large or complex pedigrees, or large (> 15) numbers of alleles per locus use the -Xms and -Xmx options to increase the space available to the java program.

The method is described in Thomas (2005), Bioinformatics.

Constructor Summary

CheckErrors()

Method Summary

static void

main(java.lang.String[] args)

Methods inherited from class alun.genapps.FindErrorProbs

outputError, outputErrorUnordered

Methods inherited from class alun.genapps.ObligatoryErrors

obligatoryError

Methods inherited from class java.lang.Object

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

Constructor Detail

CheckErrors

public CheckErrors()

Method Detail

main

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