CreateSomaticPanelOfNormals: can a panel of normals be created from more than one GenomicsDB workspace?
Dear GATK Team,
In the GATK 4.1.9.0 documentation, I see that the following is the example command for running CreateSomaticPanelOfNormals and one GenomicsDB workspace is specified:
gatk CreateSomaticPanelOfNormals -R reference.fasta -V gendb://pon_db -O pon.vcf.gz
How do I create a panel of normals from more than one GenomicsDB workspace? Is this possible or can only one be specified?
Thank you for your time and help.
-
Hi ISmolicz,
The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.
Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.
We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.
For context, check out our support policy.
-
Hi ISmolicz,
It is not possible to input multiple GenomicsDB workspaces with the CreateSomaticPanelofNormals.
However, it is possible to input multiple VCFs into one GenomicsDB workspace and then use that workspace for the CreateSomaticPanelofNormals (as outlined here). It is not supported to merge multiple GenomicsDB workspaces that are already created, though there is a discussion on github where you could provide your insights.
Sorry there is not an easier workaround solution, hope this helps.
Genevieve
Please sign in to leave a comment.
2 comments