I realized that the bed files are 0-base and the vcf files are 1-base. It seems I partially recognized this when I made the script, but maybe I didn't fix it correctly for all sites. This requires testing. At its worse, I was off by one site whenever introducing the ranges of missing data. I think this should have no effect on the conclusions of the paper, but it should be fixed if used again.
I realized that the bed files are 0-base and the vcf files are 1-base. It seems I partially recognized this when I made the script, but maybe I didn't fix it correctly for all sites. This requires testing. At its worse, I was off by one site whenever introducing the ranges of missing data. I think this should have no effect on the conclusions of the paper, but it should be fixed if used again.