# BaseCoverageDistribution

Simple walker to plot the coverage distribution per base

## Overview

Features of this walker:

• includes a smart counting of uncovered bases without visiting the uncovered loci
• includes reads with deletions in the loci (optionally can be turned off)
• ### Input

The BAM file and an optional interval list (works for WGS as well)

### Output

A GATK Report with the coverage distribution per base

### Examples

 java -Xmx4g -jar GenomeAnalysisTK.jar \
-R ref.fasta \
-T BaseCoverageDistribution \
-I myData.bam \
-L interesting.intervals \
-fd \
-o report.grp


These Read Filters are automatically applied to the data by the Engine before processing by BaseCoverageDistribution.

### Downsampling settings

This tool applies the following downsampling settings by default.

• Mode: BY_SAMPLE
• To coverage: 1,000

## Command-line Arguments

### Inherited arguments

The arguments described in the entries below can be supplied to this tool to modify its behavior. For example, the -L argument directs the GATK engine restricts processing to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).

### BaseCoverageDistribution specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s) Default value Summary
Optional Outputs
--out
-o
NA The output GATK Report table
Optional Parameters
--minimum_base_quality
-mbq
17 minimum base quality of a base to include it in the filtered coverage distribution
--minimum_mapping_quality
-mmq
20 minimum mapping quality of a read to include it in the filtered coverage distribution
Optional Flags
--filtered_distribution
-fd
NA calculate and report the filtered coverage distribution of bases
--include_deletions
-del
NA whether or not to include reads with deletions on the loci in the pileup

### Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.

### --filtered_distribution / -fd

calculate and report the filtered coverage distribution of bases
Whether or not to calculate and output a filtered coverage distribution. Bases will be filtered according to the minimum_mapping_quality and minimum_base_quality parameters below.

boolean

### --include_deletions / -del

whether or not to include reads with deletions on the loci in the pileup
Whether or not a deletion should be counted towards the coverage of a site

boolean

### --minimum_base_quality / -mbq

minimum base quality of a base to include it in the filtered coverage distribution
The minimum base quality a base must have to be counted towards the filtered coverage of a site

byte  [ [ -∞  ∞ ] ]

### --minimum_mapping_quality / -mmq

minimum mapping quality of a read to include it in the filtered coverage distribution
The minimum mapping quality a read must have to be counted towards the filtered coverage of a site

byte  [ [ -∞  ∞ ] ]

### --out / -o

The output GATK Report table
The output GATK Report table

PrintStream