Gathers scattered VQSLOD tranches into a single file
Category Other
Overview
GatherTranches 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 |
[] | List of scattered tranches files | |
--output -O |
null | File to output the gathered tranches file to | |
Optional Tool Arguments | |||
--arguments_file |
[] | read one or more arguments files and add them to the command line | |
--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 | |
--mode |
SNP | Recalibration mode to employ | |
--truth-sensitivity-tranche -tranche |
[100.0, 99.9, 99.0, 90.0] | The levels of truth sensitivity at which to slice the data. (in percent, that is 1.0 for 1 percent) | |
--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.
--arguments_file / NA
read one or more arguments files and add them to the command line
List[File] []
--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 [ [ -∞ ∞ ] ]
--help / -h
display the help message
boolean false
--input / -I
List of scattered tranches files
R List[File] []
--mode / -mode
Recalibration mode to employ
Use either SNP for recalibrating only SNPs (emitting indels untouched in the output VCF) or INDEL for indels (emitting SNPs untouched in the output VCF). There is also a BOTH option for recalibrating both SNPs and indels simultaneously, but this is meant for testing purposes only and should not be used in actual analyses.
The --mode argument is an enumerated type (Mode), which can have one of the following values:
- SNP
- INDEL
- BOTH
Mode SNP
--output / -O
File to output the gathered tranches file to
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
Undocumented option
List[File] []
--truth-sensitivity-tranche / -tranche
The levels of truth sensitivity at which to slice the data. (in percent, that is 1.0 for 1 percent)
Add truth sensitivity slices through the call set at the given values. The default values are 100.0, 99.9, 99.0, and 90.0
which will result in 4 estimated tranches in the final call set: the full set of calls (100% sensitivity at the accessible
sites in the truth set), a 99.9% truth sensitivity tranche, along with progressively smaller tranches at 99% and 90%.
List[Double] [100.0, 99.9, 99.0, 90.0]
--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 4.0.5.0 built at 25-10-2019 02:10:54.
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