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VCF from Germline SNPs + INDELs Best Practice Workflow
Dear Firecloud team,
I just wanted to check with you couple of things regarding the Germline SNPs + INDELs production WDL/workflow. If I am planning to run this workflow with single samples only with no joint-calling in mind after this initial variant calling step would these assumptions be correct:
- Would outputting VCF from HC instead of gVCF break anything, that is would that be a considerable deviation from the best practices?
- VQSR should be skipped when working with a single sample?
- Last one, just as a sanity check this is the WDL which is considered to be the production one? I was a bit confused because of the other one in the github page.
Thanks a lot!