net.sf.varscan
Class Trio

java.lang.Object
  net.sf.varscan.Trio

public class Trio
extends java.lang.Object

A class for calling variants in a mother-father-child trio

Version:

2.4

Author:

Daniel C. Koboldt

Constructor Summary

Trio(java.lang.String[] args, java.lang.String callType)

Method Summary

java.lang.String

callTrio(java.lang.String refBase, java.util.HashMap<java.lang.String,java.lang.String> fatherCounts, java.util.HashMap<java.lang.String,java.lang.String> motherCounts, java.util.HashMap<java.lang.String,java.lang.String> childCounts, int minReads2, double minVarFreq, int minAvgQual, double pValueThreshold, double minFreqForHom)

Methods inherited from class java.lang.Object

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

Constructor Detail

Trio

public Trio(java.lang.String[] args,
            java.lang.String callType)

Method Detail

callTrio

public java.lang.String callTrio(java.lang.String refBase,
                                 java.util.HashMap<java.lang.String,java.lang.String> fatherCounts,
                                 java.util.HashMap<java.lang.String,java.lang.String> motherCounts,
                                 java.util.HashMap<java.lang.String,java.lang.String> childCounts,
                                 int minReads2,
                                 double minVarFreq,
                                 int minAvgQual,
                                 double pValueThreshold,
                                 double minFreqForHom)