Get the maximum likelihood estimates of artifact prior probabilities in the orientation bias mixture model filter
Category Short Variant Discovery
Overview
Learn the prior probability of read orientation artifact from the output of CollectF1R2Counts of Mutect2 Details of the model may be found in docs/mutect/mutect.pdf.Usage Examples
gatk LearnReadOrientationModel \ -I f1r2.tar.gz \ -O artifact-prior.tar.gz Note that the -I argument may be specified multiple times, as in the case of learning a model from multiple scatters of the same sample. The input F1R2 tar.gz counts can be generated by CollectF1R2Counts or by Mutect2, with the --f1r2-tar-gz argument. If the inputs contains F1R2 counts for multiple samples then the output file contains learned artifact priors for the same samples.LearnReadOrientationModel 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 |
One or more .tar.gz containing outputs of CollectF1R2Counts | ||
--output -O |
tar.gz of artifact prior tables | ||
Optional Tool Arguments | |||
--arguments_file |
read one or more arguments files and add them to the command line | ||
--convergence-threshold |
1.0E-4 | Stop the EM when the distance between parameters between iterations falls below this value | |
--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 | |
--max-depth |
200 | sites with depth higher than this value will be grouped | |
--num-em-iterations |
20 | give up on EM after this many iterations | |
--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] []
--convergence-threshold
Stop the EM when the distance between parameters between iterations falls below this value
double 1.0E-4 [ [ -∞ ∞ ] ]
--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
One or more .tar.gz containing outputs of CollectF1R2Counts
R List[File] []
--max-depth
sites with depth higher than this value will be grouped
int 200 [ [ -∞ ∞ ] ]
--num-em-iterations
give up on EM after this many iterations
int 20 [ [ -∞ ∞ ] ]
--output / -O
tar.gz of artifact prior tables
R File null
--QUIET
Whether to suppress job-summary info on System.err.
Boolean false
--showHidden / -showHidden
display hidden arguments
boolean false
--tmp-dir
Temp directory to use.
GATKPath 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
display the version number for this tool
boolean false
GATK version 4.2.5.0-SNAPSHOT built at Mon, 7 Feb 2022 11:18:01 -0500.
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