BaseCoverageDistribution

Simple walker to plot the coverage distribution per base

Category Diagnostics and Quality Control Tools

Traversal LocusWalker

PartitionBy LOCUS


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
     

    Additional Information

    Read filters

    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
    stdout 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
    false calculate and report the filtered coverage distribution of bases
    --include_deletions
     -del
    true 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  false


    --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  true


    --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  17  [ [ -?  ? ] ]


    --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  20  [ [ -?  ? ] ]


    --out / -o

    The output GATK Report table
    The output GATK Report table

    PrintStream  stdout


    See also Guide Index | Tool Documentation Index | Support Forum

    GATK version 3.1-1-g07a4bf8 built at 2014/03/18 07:00:36. GTD: NA