Gathers scattered VQSLOD tranches into a single file
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|
|||List of scattered tranches files|
|null||File to output the gathered tranches file to|
|Optional Tool Arguments|
||||read one or more arguments files and add them to the command line|
|20||If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection|
||""||Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.|
|false||display the help message|
||SNP||Recalibration mode to employ|
|[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)|
||false||display the version number for this tool|
|Optional Common Arguments|
||null||A configuration file to use with the GATK.|
||false||Whether to suppress job-summary info on System.err.|
||null||Temp directory to use.|
|false||Whether to use the JdkDeflater (as opposed to IntelDeflater)|
|false||Whether to use the JdkInflater (as opposed to IntelInflater)|
||INFO||Control verbosity of logging.|
||false||display hidden arguments|
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.
read one or more arguments files and add them to the command line
A configuration file to use with the GATK.
If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
int 20 [ [ -∞ ∞ ] ]
Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.
display the help message
List of scattered tranches files
R List[File] 
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:
File to output the gathered tranches file to
R File null
Whether to suppress job-summary info on System.err.
display hidden arguments
Temp directory to use.
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]
Whether to use the JdkDeflater (as opposed to IntelDeflater)
Whether to use the JdkInflater (as opposed to IntelInflater)
Control verbosity of logging.
The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:
display the version number for this tool
GATK version 188.8.131.52 built at Wed, 9 Oct 2019 15:19:59 -0400.