Creates plots of denoised copy ratios

Category Copy Number Variant Discovery

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Overview

Creates plots of standardized and 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 file. A plot showing both the standardized and denoised copy ratios is output. Copy ratios are only plotted up to the maximum value specified by the argument maximum-copy-ratio. Point size can be specified by the argument point-size-copy-ratio.
• 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		Input file containing denoised copy ratios (output of DenoiseReadCounts).
--output  -O		Output directory. This will be created if it does not exist.
--output-prefix		Prefix for output filenames.
--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.
--standardized-copy-ratios		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. User must have storage.buckets.get permission on the bucket being accessed.
--help  -h	false	display the help message
--maximum-copy-ratio	4.0	Maximum copy ratio to be plotted. If Infinity, the maximum copy ratio will be automatically determined.
--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.
--point-size-copy-ratio	0.2	Point size to use for plotting copy-ratio points.
--version	false	display the version number for this tool
Optional Common Arguments
--gatk-config-file		A configuration file to use with the GATK.
--QUIET	false	Whether to suppress job-summary info on System.err.
--tmp-dir		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

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

List[File]  []

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--denoised-copy-ratios

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

R File  null

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--gatk-config-file

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

Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed. User must have storage.buckets.get permission on the bucket being accessed.

String  ""

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--help / -h

display the help message

boolean  false

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--maximum-copy-ratio

Maximum copy ratio to be plotted. If Infinity, the maximum copy ratio will be automatically determined.

double  4.0  [ [ 0  ∞ ] ]

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--minimum-contig-length

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

Prefix for output filenames.

R String  null

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--point-size-copy-ratio

Point size to use for plotting copy-ratio points.

double  0.2  [ [ 0  ∞ ] ]

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--QUIET

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

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

R File  null

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--tmp-dir

Temp directory to use.

GATKPath  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

display the version number for this tool

boolean  false

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GATK version 4.2.0.0-SNAPSHOT built at Mon, 22 Feb 2021 13:44:49 -0800.