I'm trying to create something like a GVCF file for the human genome, but without the variants. It would be like:
CHROM POS BASE
I figured one way to start would be to align hg19 to itself to get a SAM file. But not sure where to go from there.
I'm guessing there might be a GVCF file out there somewhere from some project like COSMIC or 1000 Genomes. But since those are focused on variants, will they have ALL bases included?