Showing docs for version 3.7-0

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ReadClippingStats

Collect read clipping statistics

Category Diagnostics and Quality Control Tools

Traversal ReadWalker

PartitionBy READ

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Overview

This tool collects statistics about the read length, number of clipping events, and length of the clipping in all reads in the dataset.

Input

One or more BAM files.

Output

A simple tabulated text file with read length and clipping statistics for every read (or every given number of reads if the "skip" option is used).

Caveat

This tool ignores "N" events in the CIGAR string.

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Additional Information

Read filters

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

• MalformedReadFilter
• BadCigarFilter

Downsampling settings

This tool does not apply any downsampling by default.

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Command-line Arguments

Engine arguments

All tools inherit arguments from the GATK Engine' "CommandLineGATK" argument collection, which can be used to modify various aspects of the tool's function. For example, the -L argument directs the GATK engine to restrict processing to specific genomic intervals; or the -rf argument allows you to apply certain read filters to exclude some of the data from the analysis.

• CommandLineGATK

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.

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--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

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--out / -o

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

PrintStream  stdout

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--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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