How should I regenotype VCFs using vg?

[rickymagner]

Hi, I opened this question on Biostars over a week ago, and was wondering if anyone here might have an answer. Currently, the documentation in the main README isn't clear about how to go about regenotyping an existing VCF using vg. For example, the section that says using giraffe to align reads requires using autoindex, which is not allowed to be used for regenotyping. What is the correct sequence of steps for aligning reads to a graph reference using giraffe, and then regenotyping an existing VCF using those alignments?

[glennhickey]

See this part of the vg wiki

[rickymagner]

Thanks for sharing the Wiki link which addresses using regenotyping with giraffe. It looks like it requires the input VCF to be phased? Is there a best alternative in the case where my input VCF isn't phased?