Apply tranche filtering
gatk FilterVariantTranches \ -V input.vcf.gz \ --snp-truth-vcf hapmap.vcf \ --indel-truth-vcf mills.vcf \ --info-key CNN_1D \ --tranche 99.9 --tranche 99.0 --tranche 95 \ --max-sites 8000 \ -O filtered.vcf
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 | |||
--indel-truth-vcf |
null | Input file of known common INDEL sites. | |
--output -O |
null | Output VCF file | |
--snp-truth-vcf |
null | Input file of known common SNP sites. | |
--variant -V |
null | Input VCF file | |
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 | |
--info-key |
CNN_1D | The key must be in the INFO field of the input VCF. | |
--max-sites |
1200 | Maximum number of truth VCF sites to check. | |
--tranche -t |
[99.9, 99.0, 90.0] | The levels of truth sensitivity at which to slice the data. (in percents, i.e. 99.9 for 99.9 percent and 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 |
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
List[File] []
A configuration file to use with the GATK.
String null
If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
int 20 [ [ -∞ ∞ ] ]
display the help message
boolean false
Input file of known common INDEL sites.
R String null
The key must be in the INFO field of the input VCF.
String CNN_1D
Maximum number of truth VCF sites to check.
int 1200 [ [ -∞ ∞ ] ]
Output VCF file
R String null
Whether to suppress job-summary info on System.err.
Boolean false
display hidden arguments
boolean false
Input file of known common SNP sites.
R String null
Undocumented option
List[File] []
The levels of truth sensitivity at which to slice the data. (in percents, i.e. 99.9 for 99.9 percent and 1.0 for 1 percent)
List[Double] [99.9, 99.0, 90.0]
Whether to use the JdkDeflater (as opposed to IntelDeflater)
boolean false
Whether to use the JdkInflater (as opposed to IntelInflater)
boolean false
Input VCF file
R String null
Control verbosity of logging.
The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:
LogLevel INFO
display the version number for this tool
boolean false
See also General Documentation | Tool Docs Index Tool Docs Index | Support Forum
GATK version 4.0.3.0 built at 09-43-2018 09:43:10.