VCF where ref == alt

[kmhernan]

When running the dockstore-cgpwgs workflow on some WGS samples, I have found 1 caveman VCF where there are a small number of loci where ref == alt alleles. This causes tools that validate a VCF upon reading it to throw an exception. Isn't the appropriate way to do this to set the alt allele to . ? Also, why is this even happening? For now, I will have to go and remove these loci from the vcf before processing, but I wanted to put it on your radar.