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- 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.
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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)
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Method Detail
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getMeanDepth
static double getMeanDepth(String gvcfFile)
Simple method to compute the mean of the depths.
- Parameters:
gvcfFile
- Full file path to the gvcf file
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getMeanDepth
static double getMeanDepth(String gvcfFile, String intervalFile)
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getModeDepth
static int getModeDepth(String gvcfFile)
Simple method to get the mode of the depth.
- Parameters:
gvcfFile
- Full file path to the gvcf file
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getModeDepth
static int getModeDepth(String gvcfFile, String intervalFile)
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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
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getMedianDepth
static int getMedianDepth(String gvcfFile, String intervalFile)
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