Documentation

ReadClippingStats

Read clipping statistics for all reads.

Category Diagnostics and Quality Control Tools

Traversal ReadWalker

PartitionBy READ


Overview

Walks over the input reads, printing out statistics about the read length, number of clipping events, and length of the clipping to the output stream. Note: Ignores N's in the Cigar string.

Input

One or more BAM files

Output

A simple tabulated text file with read length and clipping statistics for every read (or every N reads if the "skip" option is used) User: depristo Date: May 5, 2010 Time: 12:16:41 PM

Additional Information

Read filters

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

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).

ReadClippingStats 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
Optional Flags
--include_unmapped
 -u
false Include unmapped reads in the analysis
Advanced Parameters
--skip
1 Do not print all reads, skip some.

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.


--include_unmapped / -u

Include unmapped reads in the analysis
when this flag is set (default), statistics will be collected on unmapped reads as well. The default behavior is to ignore unmapped reads."

boolean  false


--out / -o

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

PrintStream  stdout


--skip / -skip

Do not print all reads, skip some.
print every read whose read number is divisible by SKIP. READ_NUMBER % SKIP == 0. First read in the file has read number = 1, second is 2, third is 3, ... A value of 1 means print every read. A value of 1000 means print every 1000th read.

int  1  [ [ -?  ? ] ]


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