A quality list of candidate SNPs (ususally common SNPs) are important for mode 1. If a list of genotyped SNPs is available, it can be used to pile up. Alternatively, for human, common SNPs in population that have been idenetified from consortiums can also be very good candidates, e.g., gnomAD and 1000 Genome Project. For the latter, we have compiled a list of 7.4 million common variants (AF>5%) with script SNPlist_1Kgenome.sh and stored in folder SNPlist.
In case you want to lift over SNP positions in vcf file from one genome build to another, see our LiftOver_vcf wrap function.