Calls copy-ratio segments as amplified, deleted, or copy-number neutral

Category Copy Number Variant Discovery

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Overview

Calls copy-ratio segments as amplified, deleted, or copy-number neutral.

This is a relatively naive caller that takes the modeled-segments output of ModelSegments and performs a simple statistical test on the segmented log2 copy ratios to call amplifications and deletions, given a specified range for determining copy-number neutral segments. This caller is based on the calling functionality of ReCapSeg.

If provided ModelSegments results that incorporate allele-fraction data, i.e. data with presumably improved segmentation, the statistical test performed by CallCopyRatioSegments ignores the modeled minor-allele fractions when making calls.

Input

• Copy-ratio-segments .cr.seg file from ModelSegments. This is a tab-separated values (TSV) file with a SAM-style header containing a read group sample name, a sequence dictionary, a row specifying the column headers contained in CopyRatioSegmentCollection.CopyRatioSegmentTableColumn, and the corresponding entry rows.

Output

• Called copy-ratio-segments file. This is a tab-separated values (TSV) file with a SAM-style header containing a read group sample name, a sequence dictionary, a row specifying the column headers contained in CalledCopyRatioSegmentCollection.CalledCopyRatioSegmentTableColumn, and the corresponding entry rows.

Usage example

     gatk CallCopyRatioSegments \
          -I tumor.cr.seg \
          -O tumor.called.seg
 

CallCopyRatioSegments 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
--input  -I	null	Input file containing copy-ratio segments (.cr.seg output of ModelSegments).
--output  -O	null	Output file for called copy-ratio segments.
Optional Tool Arguments
--arguments_file	[]	read one or more arguments files and add them to the command line
--calling-copy-ratio-z-score-threshold	2.0	Threshold on z-score of non-log2 copy ratio used for calling segments.
--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
--neutral-segment-copy-ratio-lower-bound	0.9	Lower bound on non-log2 copy ratio used for determining copy-neutral segments.
--neutral-segment-copy-ratio-upper-bound	1.1	Upper bound on non-log2 copy ratio used for determining copy-neutral segments.
--outlier-neutral-segment-copy-ratio-z-score-threshold	2.0	Threshold on z-score of non-log2 copy ratio used for determining outlier copy-neutral segments. If non-log2 copy ratio z-score is above this threshold for a copy-neutral segment, it is considered an outlier and not used in the calculation of the length-weighted mean and standard deviation used for calling.
--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.

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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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--calling-copy-ratio-z-score-threshold / NA

Threshold on z-score of non-log2 copy ratio used for calling segments.

double  2.0  [ [ 0  ∞ ] ]

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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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--help / -h

display the help message

boolean  false

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--input / -I

Input file containing copy-ratio segments (.cr.seg output of ModelSegments).

R File  null

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--neutral-segment-copy-ratio-lower-bound / NA

Lower bound on non-log2 copy ratio used for determining copy-neutral segments.

double  0.9  [ [ 0  ∞ ] ]

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--neutral-segment-copy-ratio-upper-bound / NA

Upper bound on non-log2 copy ratio used for determining copy-neutral segments.

double  1.1  [ [ 0  ∞ ] ]

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--outlier-neutral-segment-copy-ratio-z-score-threshold / NA

Threshold on z-score of non-log2 copy ratio used for determining outlier copy-neutral segments. If non-log2 copy ratio z-score is above this threshold for a copy-neutral segment, it is considered an outlier and not used in the calculation of the length-weighted mean and standard deviation used for calling.

double  2.0  [ [ 0  ∞ ] ]

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--output / -O

Output file for called copy-ratio segments.

R File  null

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--QUIET / NA

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

Boolean  false

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--showHidden / -showHidden

display hidden arguments

boolean  false

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--TMP_DIR / NA

Undocumented option

List[File]  []

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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 4.0.5.1 built at 25-59-2019 01:59:53.