Referce SNPs in the same vcf file than the alternative alleles
I have a simple question, I have several individuals sequenced with GBS and I want to call SNPs from all of them. Using the best practice approach, that includes to run the HC in GVCF mode and then make the joint calling on multiple GVCFs I am going to end with a multisample VCF file.
What I want to know is if in the multi sample VCF file are going to be included the reference SNPs (those ones in the reference genome) and the alternative alleles. Because the nature of my individuals I expect per site the 25% with my individuals with the alternative allele and 75% with the reference allele and for me is important to call both. With these best practice process, of course If I have enough data in the site and playing with the filtering process after. I am going to be able to obtain both alleles per site? .