Creates plots of denoised and segmented copy-ratio and minor-allele-fraction estimates

Category Copy Number Variant Discovery

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Overview

Creates plots of denoised and segmented copy-ratio and minor-allele-fraction estimates.

Inputs

• Modeled-segments file from ModelSegments.
• (Optional) Denoised-copy-ratios file from DenoiseReadCounts. If allelic counts are not provided, then this is required.
• (Optional) Allelic-counts file containing the counts at sites genotyped as heterozygous (.hets.tsv output of ModelSegments). If denoised copy ratios are not provided, then this is required.
• 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.

Output

• Modeled-segments-plot file. This shows the input denoised copy ratios and/or alternate-allele fractions as points, as well as box plots for the available posteriors in each segment. The colors of the points alternate with the segmentation.

Usage examples

     gatk PlotModeledSegments \
          --denoised-copy-ratios tumor.denoisedCR.tsv \
          --allelic-counts tumor.hets.tsv \
          --segments tumor.modelFinal.seg \
          --sequence-dictionary contigs_to_plot.dict \
          --output-prefix tumor \
          -O output_dir
 

     gatk PlotModeledSegments \
          --denoised-copy-ratios tumor.denoisedCR.tsv \
          --segments tumor.modelFinal.seg \
          --sequence-dictionary contigs_to_plot.dict \
          --output-prefix tumor \
          -O output_dir
 

     gatk PlotModeledSegments \
          --allelic-counts normal.hets.tsv \
          --segments normal.modelFinal.seg \
          --sequence-dictionary contigs_to_plot.dict \
          --output-prefix normal \
          -O output_dir
 

PlotModeledSegments 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
--output  -O	null	Output directory. This will be created if it does not exist.
--output-prefix	null	Prefix for output filenames.
--segments	null	Input file containing modeled segments (output of ModelSegments).
--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.
Optional Tool Arguments
--allelic-counts	null	Input file containing allelic counts at heterozygous sites (.hets.tsv output of ModelSegments).
--arguments_file	[]	read one or more arguments files and add them to the command line
--denoised-copy-ratios	null	Input file containing denoised copy ratios (output of DenoiseReadCounts).
--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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--allelic-counts / NA

Input file containing allelic counts at heterozygous sites (.hets.tsv output of ModelSegments).

File  null

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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).

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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--segments / NA

Input file containing modeled segments (output of ModelSegments).

R File  null

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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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--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 4.1.6.0-SNAPSHOT built at Thu, 2 Apr 2020 14:54:17 -0400.