Introduction Read in vcf header Parse out chr / contig sizes Split chr above 3e7 base pairs into equal(ish) size pieces print coordinates given a chromosome / contig calculate coordinates print ’em output ’em for python input (Snakemake) rscript Using the script output sessionInfo() Introduction bcftools view -r 1:40000-50000 vcf.gz will output (to stdout) a vcf containing the header and variants on chromosome 1 between coordinates 40,000 and 50,000 base pairs.