Package 

Class ComputeMedianAnnotation

  • All Implemented Interfaces:
    
public class ComputeMedianAnnotation

    Simple Utility to Extract Mean, Median and Mode for Depth in a GVCF file Currently supports only DP as defined in the FORMAT Tag. If the value is missing, it will not count anything. For a reference block, it will count the depth for each base pair in the block. For a variant, it will count the depth once. Created by zrm22 on 6/30/17.

    • Nested Class Summary

      Nested Classes 
      Modifier and Type Class Description

    • Field Summary

      Fields 
      Modifier and Type Field Description

    • Constructor Summary

      Constructors 
      Constructor Description

    • Enum Constant Summary

      Enum Constants 
      Enum Constant Description

    • Method Summary

      Modifier and Type Method Description
      static double getMeanDepth(String gvcfFile) Simple method to compute the mean of the depths.
      static double getMeanDepth(String gvcfFile, String intervalFile)
      static int getModeDepth(String gvcfFile) Simple method to get the mode of the depth.
      static int getModeDepth(String gvcfFile, String intervalFile)
      static int getMedianDepth(String gvcfFile) Simple method to calculate the Median depth for a GVCF file.
      static int getMedianDepth(String gvcfFile, String intervalFile)

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

    • Method Detail

      • getMeanDepth

         static double getMeanDepth(String gvcfFile)

        Simple method to compute the mean of the depths.

        Parameters:
        gvcfFile - Full file path to the gvcf file

      • getModeDepth

         static int getModeDepth(String gvcfFile)

        Simple method to get the mode of the depth.

        Parameters:
        gvcfFile - Full file path to the gvcf file

      • getMedianDepth

         static int getMedianDepth(String gvcfFile)

        Simple method to calculate the Median depth for a GVCF file.

        Parameters:
        gvcfFile - Full file path to the gvcf file