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 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.
- 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 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 | |
--gcs-project-for-requester-pays |
"" | Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be 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 |
null | A configuration file to use with the GATK. | |
--QUIET |
false | Whether to suppress job-summary info on System.err. | |
--tmp-dir |
null | 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 / NA
read one or more arguments files and add them to the command line
List[File] []
--calling-copy-ratio-z-score-threshold / NA
Threshold on z-score of non-log2 copy ratio used for calling segments.
double 2.0 [ [ 0 ∞ ] ]
--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 [ [ -∞ ∞ ] ]
--gcs-project-for-requester-pays / NA
Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be 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 / NA
Lower bound on non-log2 copy ratio used for determining copy-neutral segments.
double 0.9 [ [ 0 ∞ ] ]
--neutral-segment-copy-ratio-upper-bound / NA
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 / 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 ∞ ] ]
--output / -O
Output file for called copy-ratio segments.
R File null
--QUIET / NA
Whether to suppress job-summary info on System.err.
Boolean false
--showHidden / -showHidden
display hidden arguments
boolean false
--tmp-dir / NA
Temp directory to use.
String 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 / NA
display the version number for this tool
boolean false
GATK version 4.1.1.0 built at Sat, 23 Nov 2019 17:29:19 -0500.
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