Creates plots of denoised copy ratios

Category Copy Number Variant Discovery

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Overview

Creates plots of denoised copy ratios. The tool also generates various denoising metrics.

Inputs

• Standardized-copy-ratios from DenoiseReadCounts.
• Denoised-copy-ratios from DenoiseReadCounts.
• Sequence-dictionary file. This determines the order and representation of contigs in the plot.
• Output prefix. This is used as the basename for output files.
• Output directory. This will be created if it does not exist.

Outputs

• Denoised-plot files. Two versions of a plot showing both the standardized and denoised copy ratios are output; the first covers the entire range of the copy ratios, while the second is limited to copy ratios within [0, 4].
• Median-absolute-deviation files. These files contain the median absolute deviation (MAD) for both the standardized (.standardizedMAD.txt) and denoised (.denoisedMAD.txt) copy ratios, the change between the two (.deltaMAD.txt), and the change between the two scaled by the standardized MAD (.deltaScaledMAD.txt).

Usage example

     gatk PlotDenoisedCopyRatios \
          --standardized-copy-ratios tumor.standardizedCR.tsv \
          --denoised-copy-ratios tumor.denoisedCR.tsv \
          --sequence-dictionary contigs_to_plot.dict \
          --output-prefix tumor \
          -O output_dir
 

PlotDenoisedCopyRatios 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
Required Arguments
--denoised-copy-ratios	null	Input file containing denoised copy ratios (output of DenoiseReadCounts).
--output  -O	null	Output directory. This will be created if it does not exist.
--output-prefix	null	Prefix for output filenames.
--sequence-dictionary	null	File containing a sequence dictionary, which specifies the contigs to be plotted and their relative lengths. The sequence dictionary must be a subset of those contained in other input files. Contigs will be plotted in the order given. Contig names should not include the string "CONTIG_DELIMITER". The tool only considers contigs in the given dictionary for plotting, and data for contigs absent in the dictionary generate only a warning. In other words, you may modify a reference dictionary for use with this tool to include only contigs for which plotting is desired, and sort the contigs to the order in which the plots should display the contigs.
--standardized-copy-ratios	null	Input file containing standardized copy ratios (output of DenoiseReadCounts).
Optional Tool Arguments
--arguments_file	[]	read one or more arguments files and add them to the command line
--gcs-max-retries  -gcs-retries	20	If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
--gcs-project-for-requester-pays	""	Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.
--help  -h	false	display the help message
--minimum-contig-length	1000000	Threshold length (in bp) for contigs to be plotted. Contigs with lengths less than this threshold will not be plotted. This can be used to filter out mitochondrial contigs, unlocalized contigs, etc.
--version	false	display the version number for this tool
Optional Common Arguments
--gatk-config-file	null	A configuration file to use with the GATK.
--QUIET	false	Whether to suppress job-summary info on System.err.
--tmp-dir	null	Temp directory to use.
--use-jdk-deflater  -jdk-deflater	false	Whether to use the JdkDeflater (as opposed to IntelDeflater)
--use-jdk-inflater  -jdk-inflater	false	Whether to use the JdkInflater (as opposed to IntelInflater)
--verbosity	INFO	Control verbosity of logging.
Advanced Arguments
--showHidden	false	display hidden arguments

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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--arguments_file / NA

read one or more arguments files and add them to the command line

List[File]  []

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--denoised-copy-ratios / NA

Input file containing denoised copy ratios (output of DenoiseReadCounts).

R File  null

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--gatk-config-file / NA

A configuration file to use with the GATK.

String  null

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--gcs-max-retries / -gcs-retries

If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection

int  20  [ [ -∞  ∞ ] ]

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--gcs-project-for-requester-pays / NA

Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.

String  ""

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--help / -h

display the help message

boolean  false

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--minimum-contig-length / NA

Threshold length (in bp) for contigs to be plotted. Contigs with lengths less than this threshold will not be plotted. This can be used to filter out mitochondrial contigs, unlocalized contigs, etc.

int  1000000  [ [ 0  ∞ ] ]

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--output / -O

Output directory. This will be created if it does not exist.

R File  null

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--output-prefix / NA

Prefix for output filenames.

R String  null

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--QUIET / NA

Whether to suppress job-summary info on System.err.

Boolean  false

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--sequence-dictionary / -sequence-dictionary

File containing a sequence dictionary, which specifies the contigs to be plotted and their relative lengths. The sequence dictionary must be a subset of those contained in other input files. Contigs will be plotted in the order given. Contig names should not include the string "CONTIG_DELIMITER". The tool only considers contigs in the given dictionary for plotting, and data for contigs absent in the dictionary generate only a warning. In other words, you may modify a reference dictionary for use with this tool to include only contigs for which plotting is desired, and sort the contigs to the order in which the plots should display the contigs.

R File  null

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--showHidden / -showHidden

display hidden arguments

boolean  false

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--standardized-copy-ratios / NA

Input file containing standardized copy ratios (output of DenoiseReadCounts).

R File  null

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--tmp-dir / NA

Temp directory to use.

GATKPathSpecifier  null

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--use-jdk-deflater / -jdk-deflater

Whether to use the JdkDeflater (as opposed to IntelDeflater)

boolean  false

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--use-jdk-inflater / -jdk-inflater

Whether to use the JdkInflater (as opposed to IntelInflater)

boolean  false

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--verbosity / -verbosity

Control verbosity of logging.

The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:

ERROR

WARNING

INFO

DEBUG

LogLevel  INFO

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--version / NA

display the version number for this tool

boolean  false

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GATK version 4.1.5.0-SNAPSHOT built at Wed, 4 Mar 2020 13:47:07 -0500.