Documentation

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.

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).

CountLoci 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 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

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

PrintStream  stdout


See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.2-2-gec30cee built at 2014/07/17 17:54:48. GTD: NA