User error in GATK CreateSomaticPanelOfNormals

Question

[Hasib]

Hi. I ran the gatk CreateSomaticPanelOfNormals program to create a PoN from 4 normal samples. I added each of the 4 files individually with the -vcfs option. When I run the command, it shows an user error that vcfs is not a recognized option. My software version is 4.2.4.

How do I resolve this? How can I add my vcf.gz files individually and avoid creating a .arg or .list file beforehand?

The command I ran:

gatk CreateSomaticPanelOfNormals \
-vcfs DU_001_PoN.vcf.gz \
- vcfs DU_002_PoN.vcf.gz \
-vcfs DU_003_PoN.vcf.gz \
-vcfs DU_004_PoN.vcf.gz \
-O DU_BDUC_PoN.vcf.gz

[Jianying]

Were you able to fix it? I have the exactly same question.

What you have maybe the older version of GATK: [https://gatk.broadinstitute.org/hc/en-us/articles/360037058172-CreateSomaticPanelOfNormals-BETA-#:~:text=Create%20a%20panel%20of%20normals,artifactual%20and%20germline%20variant%20sites.][1]

But, the new version 4.2.4.1 (I have), it has different instructions: [https://gatk.broadinstitute.org/hc/en-us/articles/5358921041947-CreateSomaticPanelOfNormals-BETA- ][1]

It seems intuitive, but, there was a parameter "-L", is not required from the helpdoc, but it complains when I did without, so I am stuck here.

[Hasib]

Hi, sorry for the late reply. I ended up not creating a PoN from my own normal sample and downloaded necessary PoN and reference genome file from this link: https://console.cloud.google.com/storage/browser/gatk-best-practices/somatic-hg38;tab=objects?prefix=&forceOnObjectsSortingFiltering=false

Hope it helps!