BaseCoverageDistribution

Simple walker to plot the coverage distribution per base.

Category Uncategorized

Traversal LocusWalker

PartitionBy LOCUS

Introduction

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

User: carneiro Date: 1/27/13 Time: 11:16 AM

Additional Information

Read filters

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

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).

CommandLineGATK

BaseCoverageDistribution specific arguments

This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.

Name	Type	Default value	Summary
Required
--out	PrintStream	stdout	The output GATK Report table
Optional
--filtered_distribution	boolean	false	calculate and report the filtered coverage distribution of bases
--include_deletions	boolean	true	whether or not to include reads with deletions on the loci in the pileup
--minimum_base_quality	byte	17	minimum base quality of a base to include it in the filtered coverage distribution
--minimum_mapping_quality	byte	20	minimum mapping quality of a read to include it in the filtered coverage distribution

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 ( boolean with default value false )

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.

--include_deletions / -del ( boolean with default value true )

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

--minimum_base_quality / -mbq ( byte with default value 17 )

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

--minimum_mapping_quality / -mmq ( byte with default value 20 )

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

--out / -o ( PrintStream with default value stdout )

The output GATK Report table. The output GATK Report table

GATK version 2.4-9-ge182083 built at 2013/03/19 07:40:48.