Get the maximum likelihood estimates of artifact prior probabilities in the orientation bias mixture model filter

Category Short Variant Discovery

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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.

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--arguments_file

read one or more arguments files and add them to the command line

List[File]  []

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--convergence-threshold

Stop the EM when the distance between parameters between iterations falls below this value

double  1.0E-4  [ [ -∞  ∞ ] ]

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--gatk-config-file

A configuration file to use with the GATK.

String  null

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--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  [ [ -∞  ∞ ] ]

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--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  ""

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--help / -h

display the help message

boolean  false

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--input / -I

One or more .tar.gz containing outputs of CollectF1R2Counts

R List[File]  []

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--max-depth

sites with depth higher than this value will be grouped

int  200  [ [ -∞  ∞ ] ]

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--num-em-iterations

give up on EM after this many iterations

int  20  [ [ -∞  ∞ ] ]

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--output / -O

tar.gz of artifact prior tables

R File  null

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--QUIET

Whether to suppress job-summary info on System.err.

Boolean  false

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--showHidden / -showHidden

display hidden arguments

boolean  false

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--tmp-dir

Temp directory to use.

GATKPath  null

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--use-jdk-deflater / -jdk-deflater

Whether to use the JdkDeflater (as opposed to IntelDeflater)

boolean  false

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--use-jdk-inflater / -jdk-inflater

Whether to use the JdkInflater (as opposed to IntelInflater)

boolean  false

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--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

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--version

display the version number for this tool

boolean  false

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GATK version 4.2.2.0-SNAPSHOT built at Thu, 19 Aug 2021 09:49:28 -0700.