GATK Panel Of Normals (PoN)

Question

[Barry Digby]

I keep running into the following error when trying to follow GATKs 'best practice workflow' for Somatic short variant discovery (SNVs + Indels):

Warning: CreateSomaticPanelOfNormals is a BETA tool and is not yet ready for use in production

I have tried both gatk-4.0.11.0 and gatk-4.0.2.1, I have supplied a .list for --vcfs, and tried supplying each file for --vcfs.

I have Normal, Tumor, Recurrence samples for each patient. If I cannot get CreateSomaticPanelOfNormals working, can I emit it downstream for Mutect2?

[Pierre Lindenbaum]

I only see a warning. "(this tool) is not yet ready for use in production"

[MS]

Hi i am taking the same warning aswell but it does not work (https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_walkers_mutect_CreateSomaticPanelOfNormals.php ). And i also find a lot of version of CreateSomaticPanelOfNormal.

I am using gatk-4.1.2.0 version. When i also try following commonds it returns A USER ERROR has occurred: v is not a recognized option

Create PONs: gatk Mutect2 -R ref.fasta -I normal1.recalib.bam -normal normal1 -disable-read-filter MateOnSameContigOrNoMappedMateReadFilter -L e/targets.interval_list -O normal1.vcf.gz

Collect PONs: gatk CreateSomaticPanelOfNormals -vcfs normal1.vcf.gz -vcfs normal2.vcf.gz -vcfs normal3.vcf.gz -O all_pon.vcf.gz

Can you suggest which commonds should i use for gatk-4.1.2.0 version?

[Barry Digby]

The error output tells you what the problem is. -v is not a recognized option. You probably want to use -V instead of -vcfs

Uppercase, not lower case.

[MS]

when I tried -V again error occurs: A USER ERROR has occurred: Argument '[V, variant]' cannot be specified more than once.

Also when I try new syntax : Step 1. Run Mutect2 in tumor-only mode for each normal sample: $gatk Mutect2 -R Ref.fasta -I normal1.bam -O normal1.vcf.gz $gatk Mutect2 -R Ref.fasta -I normal2.bam -O normal2.vcf.gz

Step 2. Create a GenomicsDB from the normal Mutect2 calls. $gatk GenomicsDBImport -R ref.fasta -L targets.interval_list --genomicsdb-workspace-path pon_db -V normal1.vcf.gz -V normal2.vcf.gz

Step 3. Combine the normal calls using CreateSomaticPanelOfNormals. $gatk CreateSomaticPanelOfNormals -R ref.fasta -V gendb://pon_db -O all_pon.vcf.gz

This time it does not create all_pon.vcf.gz and gives following error:

 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

   Warning: CreateSomaticPanelOfNormals is a BETA tool and is not yet ready for use in production

   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!


11:39:55.825 INFO  CreateSomaticPanelOfNormals - Initializing engine
11:39:56.382 INFO  CreateSomaticPanelOfNormals - Shutting down engine
[May 6, 2019 11:39:56 AM EET] org.broadinstitute.hellbender.tools.walkers.mutect.CreateSomaticPanelOfNormals done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=1175977984
java.lang.IllegalStateException: There is no genome data stored in the database
    at org.genomicsdb.reader.GenomicsDBFeatureReader.<init>(GenomicsDBFeatureReader.java:75)
    at org.broadinstitute.hellbender.engine.FeatureDataSource.getGenomicsDBFeatureReader(FeatureDataSource.java:374)
    at org.broadinstitute.hellbender.engine.FeatureDataSource.getFeatureReader(FeatureDataSource.java:296)
    at org.broadinstitute.hellbender.engine.FeatureDataSource.<init>(FeatureDataSource.java:256)
    at org.broadinstitute.hellbender.engine.VariantWalker.initializeDrivingVariants(VariantWalker.java:58)
    at org.broadinstitute.hellbender.engine.VariantWalkerBase.initializeFeatures(VariantWalkerBase.java:55)
    at org.broadinstitute.hellbender.engine.GATKTool.onStartup(GATKTool.java:697)
    at org.broadinstitute.hellbender.engine.VariantWalker.onStartup(VariantWalker.java:45)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:137)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
    at org.broadinstitute.hellbender.Main.main(Main.java:291)

Answer 1

[Barry Digby]

Apologies, it seems it does work. The warning message and 9s completion time threw me off