Make a panel of normals for use with Mutect2

Category Variant Filtering

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Overview

Create a panel of normals (PoN) containing germline and artifactual sites for use with Mutect2.

The tool takes multiple normal sample callsets produced by Mutect2's tumor-only mode and collates them into a single variant call format (VCF) file of false positive calls. The PoN captures common artifactual and germline variant sites. Mutect2 then uses the PoN to filter variants at the site-level.

This contrasts with the GATK3 workflow, which uses CombineVariants to retain variant sites called in at least two samples and then uses Picard MakeSitesOnlyVcf to simplify the callset for use as a PoN.

Examples

Step 1. Run Mutect2 in tumor-only mode for each normal sample.

 gatk Mutect2 \
   -R ref_fasta.fa \
   -I normal1.bam \
   -tumor normal1_sample_name \
   --germline-resource af-only-gnomad.vcf.gz \
   -O normal1_for_pon.vcf.gz
 

Step 2. Create a file ending with .args extension with the paths to the VCFs from step 1, one per line. This approach is optional. It will fail if a file with an extension other than .args is used.

     normal1_for_pon.vcf.gz
     normal2_for_pon.vcf.gz
     normal3_for_pon.vcf.gz
 

Step 3. Combine the normal calls using CreateSomaticPanelOfNormals.

 gatk CreateSomaticPanelOfNormals \
   -vcfs normals_for_pon_vcf.args \
   -O pon.vcf.gz
 

Alternatively, provide each normal's VCF as separate arguments.

 gatk CreateSomaticPanelOfNormals \
   -vcfs normal1_for_pon_vcf.gz \
   -vcfs normal2_for_pon_vcf.gz \
   -vcfs normal3_for_pon_vcf.gz \
   -O pon.vcf.gz
 

The tool also accepts multiple .args files. Pass each in with the -vcfs option.

By default the tool fails if multiple vcfs have the same sample name, but the --duplicate-sample-strategy argument can be changed to ALLOW_ALL to allow duplicates or CHOOSE_FIRST to use only the first vcf with a given sample name.

See Mutect2 documentation for usage examples.

CreateSomaticPanelOfNormals 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
--output  -O	null	Output vcf
--vcfs	[]	VCFs for samples to include. May be specified either one at a time, or as one or more .args file containing multiple VCFs, one per line.
Optional Tool Arguments
--arguments_file	[]	read one or more arguments files and add them to the command line
--duplicate-sample-strategy	THROW_ERROR	How to handle duplicate samples: THROW_ERROR to fail, CHOOSE_FIRST to use the first vcf with each sample name, ALLOW_ALL to use all samples regardless of duplicate sample names.
--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
--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.

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--arguments_file / NA

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

List[File]  []

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--duplicate-sample-strategy / NA

How to handle duplicate samples: THROW_ERROR to fail, CHOOSE_FIRST to use the first vcf with each sample name, ALLOW_ALL to use all samples regardless of duplicate sample names.
How to handle duplicate samples: THROW_ERROR to fail, CHOOSE_FIRST to use the first vcf with each sample name, ALLOW_ALL to use all samples regardless of duplicate sample names."

The --duplicate-sample-strategy argument is an enumerated type (DuplicateSampleStrategy), which can have one of the following values:

THROW_ERROR

CHOOSE_FIRST

ALLOW_ALL

DuplicateSampleStrategy  THROW_ERROR

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--gatk-config-file / NA

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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--help / -h

display the help message

boolean  false

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--output / -O

Output vcf

R File  null

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--QUIET / NA

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 / NA

Undocumented option

List[File]  []

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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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--vcfs / -vcfs

VCFs for samples to include. May be specified either one at a time, or as one or more .args file containing multiple VCFs, one per line.
The VCFs can be input as either one or more .args file(s) containing one VCF per line, or VCFs can be specified explicitly on the command line.

R Set[File]  []

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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 / NA

display the version number for this tool

boolean  false

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GATK version 4.0.0.0 built at 27-36-2019 11:36:13.