Creates plots of denoised and segmented copy-ratio and minor-allele-fraction estimates
Category Copy Number Variant Discovery
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.
Outputs
- 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. Copy ratios are only plotted up to the maximum value specified by the argument maximum-copy-ratio. Point sizes can be specified by the arguments point-size-copy-ratio and point-size-allele-fraction.
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 |
Output directory. This will be created if it does not exist. | ||
--output-prefix |
Prefix for output filenames. | ||
--segments |
Input file containing modeled segments (output of ModelSegments). | ||
--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. | ||
Optional Tool Arguments | |||
--allelic-counts |
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 |
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. 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-allele-fraction |
0.4 | Point size to use for plotting allele-fraction points. | |
--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.
--allelic-counts
Input file containing allelic counts at heterozygous sites (.hets.tsv output of ModelSegments).
File null
--arguments_file
read one or more arguments files and add them to the command line
List[File] []
--denoised-copy-ratios
Input file containing denoised copy ratios (output of DenoiseReadCounts).
File null
--gatk-config-file
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 [ [ -∞ ∞ ] ]
--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 ""
--help / -h
display the help message
boolean false
--maximum-copy-ratio
Maximum copy ratio to be plotted. If Infinity, the maximum copy ratio will be automatically determined.
double 4.0 [ [ 0 ∞ ] ]
--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 ∞ ] ]
--output / -O
Output directory. This will be created if it does not exist.
R File null
--output-prefix
Prefix for output filenames.
R String null
--point-size-allele-fraction
Point size to use for plotting allele-fraction points.
double 0.4 [ [ 0 ∞ ] ]
--point-size-copy-ratio
Point size to use for plotting copy-ratio points.
double 0.2 [ [ 0 ∞ ] ]
--QUIET
Whether to suppress job-summary info on System.err.
Boolean false
--segments
Input file containing modeled segments (output of ModelSegments).
R File null
--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
--tmp-dir
Temp directory to use.
GATKPath null
--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
display the version number for this tool
boolean false
GATK version 4.2.4.0-SNAPSHOT built at Thu, 16 Dec 2021 11:57:48 -0800.
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