PlotACNVResults

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

Category Copy Number Analysis Tools


Overview

Plot segmented copy-ratio and minor-allele-fraction results.

The order and representation of contigs in plots follows the contig ordering within the required reference sequence dictionary.

Example

 gatk-launch --javaOptions "-Xmx4g" PlotACNVResults \
   --hets tumor.hets.tsv \
   --tangentNormalized tn_coverage.tn.tsv \
   --segments acnv_segments.seg \
   -SD ref_fasta.dict \
   --output folder_name \
   --outputPrefix basename
 

The --output parameter specifies a directory.

PlotACNVResults 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
--hets
 -HET
null File containing het SNP positions, ref counts, and alt counts, produced by GetHetCoverage/GetBayesianHetCoverage.
--output
 -O
null Output directory.
--outputPrefix
 -pre
null Prefix for output filenames.
--segments
 -S
null File containing segmented regions of the genome, produced by AllelicCNV.
--sequenceDictionaryFile
 -SD
null File containing the reference sequence dictionary (used to determine relative contig lengths). 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.
--tangentNormalized
 -TN
null File containing tangent-normalized coverage of targets, produced by NormalizeSomaticReadCounts.
Optional Tool Arguments
--arguments_file
 -
[] read one or more arguments files and add them to the command line
--help
 -h
false display the help message
--minimumContigLength
 -minContigLength
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
--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 / -

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

List[File]  []


--help / -h

display the help message

boolean  false


--hets / -HET

File containing het SNP positions, ref counts, and alt counts, produced by GetHetCoverage/GetBayesianHetCoverage.

R File  null


--minimumContigLength / -minContigLength

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


--outputPrefix / -pre

Prefix for output filenames.

R String  null


--QUIET / -

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

Boolean  false


--segments / -S

File containing segmented regions of the genome, produced by AllelicCNV.

R File  null


--sequenceDictionaryFile / -SD

File containing the reference sequence dictionary (used to determine relative contig lengths). 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


--tangentNormalized / -TN

File containing tangent-normalized coverage of targets, produced by NormalizeSomaticReadCounts.

R File  null


--TMP_DIR / -

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 / -

display the version number for this tool

boolean  false


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GATK version 4.beta.1-SNAPSHOT built at 28-14-2017 06:14:54.