CountLoci

Walks over the input data set, calculating the total number of covered loci for diagnostic purposes.

Category Diagnostics and Quality Control Tools

Traversal LocusWalker

PartitionBy LOCUS

Overview

This is the simplest example of a locus walker.

Input

One or more BAM files.

Output

Number of loci traversed. If an output file name is provided, then the result will be written to that file. Otherwise it will be sent to standard console output.

Examples

 java -Xmx2g -jar GenomeAnalysisTK.jar \
   -T CountLoci \
   -R ref.fasta \
   -I input.bam \
   -o output.txt \
   [-L input.intervals]

Additional Information

Read filters

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

Parallelism options

This tool can be run in multi-threaded mode using these options.

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

CountLoci 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
Optional
--out	PrintStream	stdout	An output file created by the walker. Will overwrite contents if file exists

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.

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

An output file created by the walker. Will overwrite contents if file exists.

GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.