Split VCF into separate VCFs by SNP count

There could be a more elegant way, but this could work. The first line splits up the snps into chunks of whatever size you want (-l) and then the next line loops over each file and subsets the vcf according.

bcftools query -f'%CHROMt%POSn' in.bcf | split -l 1000
for file in x*; do bcftools view -T $file -Ob in.bcf > in.$file.bcf; done