Hi,
I would like to output the results of FreeBayes as a gvcf file, but I don’t see where to specify that option.
Welcome, @Lauren_Eserman
I don’t think Freebayes is going to produce the right data, even if it could report all positions. And there isn’t a tool in Galaxy to convert vcf → gvcf, or it is new or I missed it. Others will see this topic next week and can comment more.
You could try a different variant calling tool. Maybe review and see? Help and examples are on the tool form, and you can come back here with any questions.
- DeepVariant deep learning-based variant caller
Hope this helps and we can follow up more! 
Hi @Lauren_Eserman and sorry for replying so late,
I guess nobody thought of support for the gvcf option of freebayes in the Galaxy wrapper so far, but it sounds like a reasonable request.
Regarding other variant callers, Strelka germline could be another alternative for you, which has the option to produce gvcf included already, while we’re working on a freebayes wrapper update.
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@Lauren_Eserman @jennaj as a follow-up:
a new version (1.3.10+galaxy1) of the Galaxy freebayes wrapper is now ready with new output format options for producing gVCF. This version is available since today on usegalaxy.eu and will, I assume, make it to usegalaxy.org soon as well.
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This is excellent, thank you so much! I will test it out soon.