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ReadLengthDistribution

Outputs the read lengths of all the reads in a file.

Category Diagnostics and Quality Control Tools

Traversal ReadWalker

PartitionBy READ


Overview

Generates a table with the read lengths categorized per sample. If the file has no sample information (no read groups) it considers all reads to come from the same sample.

Input

A BAM file.

Output

A human/R readable table of tab separated values with one column per sample and one row per read.

Examples

    java
      -jar GenomeAnalysisTK.jar
      -T ReadLengthDistribution
      -I example.bam
      -R reference.fasta
      -o example.tbl
  

Additional Information

Read filters

This Read Filter is automatically applied to the data by the Engine before processing by ReadLengthDistribution.

Downsampling settings

This tool does not apply any downsampling by default.


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).

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