Simple walker to plot the coverage distribution per base.
Features of this walker:
The BAM file and an optional interval list (works for WGS as well)
A GATK Report with the coverage distribution per base
java -Xmx4g -jar GenomeAnalysisTK.jar \ -R ref.fasta \ -T BaseCoverageDistribution \ -I myData.bam \ -L interesting.intervals \ -fd \ -o report.grpUser: carneiro Date: 1/27/13 Time: 11:16 AM
These Read Filters are automatically applied to the data by the Engine before processing by BaseCoverageDistribution.
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).
This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.
|--out||PrintStream||stdout||The output GATK Report table|
|--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|
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.
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.
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 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 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
The output GATK Report table. The output GATK Report table
GATK version 2.4-9-ge182083 built at 2013/03/19 07:40:48.