Creates plots of denoised copy ratios
Category Copy Number Variant Discovery
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 must be a pre-existing directory.
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. | |
--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 | |
--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 |
[] | Undocumented option | |
--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.
--arguments_file / NA
read one or more arguments files and add them to the command line
List[File] []
--denoised-copy-ratios / NA
Input file containing denoised copy ratios (output of DenoiseReadCounts).
R File null
--gatk-config-file / NA
A configuration file to use with the GATK.
String null
--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 [ [ -∞ ∞ ] ]
--help / -h
display the help message
boolean false
--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 [ [ -∞ ∞ ] ]
--output / -O
Output directory.
R String null
--output-prefix / NA
Prefix for output filenames.
R String null
--QUIET / NA
Whether to suppress job-summary info on System.err.
Boolean false
--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
--showHidden / -showHidden
display hidden arguments
boolean false
--standardized-copy-ratios / NA
Input file containing standardized copy ratios (output of DenoiseReadCounts).
R File null
--TMP_DIR / NA
Undocumented option
List[File] []
--use-jdk-deflater / -jdk-deflater
Whether to use the JdkDeflater (as opposed to IntelDeflater)
boolean false
--use-jdk-inflater / -jdk-inflater
Whether to use the JdkInflater (as opposed to IntelInflater)
boolean false
--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
--version / NA
display the version number for this tool
boolean false
GATK version 4.0.1.2 built at 02-02-2019 02:02:55.
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