CreateSomaticPanelOfNormals **BETA**

Make a panel of normals for use with Mutect2

Category VCF Tools


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-launch --javaOptions "-Xmx4g" Mutect2 \
   -R ref_fasta.fa \
   -I normal1.bam \
   -tumor normal1_sample_name \
   --germline_resource af-only-gnomad.vcf.gz \
   -L intervals.list \
   -O normal1_for_pon.vcf.gz
 

Step 2. Create a file ending with .list extension with the paths to the VCFs from step 1, one per line. This approach is optional.

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

Step 3. Combine the normal calls using CreateSomaticPanelOfNormals.

 gatk-launch --javaOptions "-Xmx4g" CreateSomaticPanelOfNormals \
   -vcfs normals_for_pon_vcf.list \
   -O pon.vcf.gz
 

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

 gatk-launch --javaOptions "-Xmx4g" 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 .list files. Pass each in with the -vcfs option.

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
--vcfsListFile
 -vcfs
[] VCFs for samples to include. May be specified either one at a time, or as one or more .list 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
--help
 -h
false display the help message
--version
 -
false display the version number for this tool
Optional Common Arguments
--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.


--arguments_file / -

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

List[File]  []


--help / -h

display the help message

boolean  false


--output / -O

Output vcf

R File  null


--QUIET / -

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

Boolean  false


--showHidden / -showHidden

display hidden arguments

boolean  false


--TMP_DIR / -

Undocumented option

List[File]  []


--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


--vcfsListFile / -vcfs

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

R Set[File]  []


--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


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GATK version 4.beta.1-SNAPSHOT built at 28-14-2017 06:14:54.