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4.6 years ago
Barry Digby ★ 1.1k
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-188.8.131.52 and gatk-184.108.40.206, 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?
I only see a warning. "(this tool) is not yet ready for use in production"
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-220.127.116.11 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-18.104.22.168 version?
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.
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: