I'm sorry if this has been answered before, but it's a simple question that I'm sure for someone more experienced would be very simple to address. I've recently received the results from my full genome sequencing in VCF format (SNP and INDEL). I would like to recreate a full genome VCF from these files (no BAM). I have the exact reference fasta used for generating the VCFs, but somehow (even after a lot of searching and experimentation) I'm still unable to get any closer to my goal. So far I've only managed to merge the two VCFs and apply the resulting file to the reference fasta, which gave me a new fasta file.
Is there any way of converting this file (or other that can be obtained from VCF) to gVCF? My goal is to extract all SNPs, not just the variations from reference.