CallCopyRatioSegments

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

Category Copy Number Variant Discovery

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 {@link 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 {@link 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 {@link 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 {@link CopyRatioSegmentCollection.CopyRatioSegmentTableColumn}, and the corresponding entry rows.

Outputs

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 {@link CalledCopyRatioSegmentCollection.CalledCopyRatioSegmentTableColumn}, and the corresponding entry rows.
CBS-formatted .igv.seg file (compatible with IGV). This is a tab-separated values (TSV) file with CBS-format column headers (see http://software.broadinstitute.org/cancer/software/genepattern/file-formats-guide#CBS) and the corresponding entry rows that can be plotted using IGV (see https://software.broadinstitute.org/software/igv/SEG). The mean log2 copy ratio is given in the SEGMENT_MEAN column.

Usage examples

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

@author David Benjamin <davidben@broadinstitute.org> @author Samuel Lee <slee@broadinstitute.org>

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

--arguments_file

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

List[File] []

--calling-copy-ratio-z-score-threshold

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

double 2.0 [ [ 0 ∞ ] ]

--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

--input / -I

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

R File null

--neutral-segment-copy-ratio-lower-bound

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

double 0.9 [ [ 0 ∞ ] ]

--neutral-segment-copy-ratio-upper-bound

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

double 1.1 [ [ 0 ∞ ] ]

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

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 ∞ ] ]