Using a VCF from an alternate germline caller for joint calline
Do you have an alternative workflow for doing joint calling using GATK when the VCF is generated from a different caller (eg. Platypus)? If so, please send us any details on how to format the VCF into GVCF and how to proceed with family trio joint calling.
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Hi James,
Thanks for writing in. Unfortunately, I am not aware of any alternative workflows other than those available in our featured workspaces or under the Broad Institute Dockstore org. I would suggest asking the expert community in any of the following forums as they may be more familiar with what you are looking for or have workflows to share:
GATK Community Forum
Biostars
Bioinformatics Stackexchange
You can also try searching through the publicly available workflows on Dockstore or the Broad Method Repository.
Best,
Samantha
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