use only the reference haplotypes (fed to -h or --haps) as reference
use a random subset of S haplotypes as reference
output every SI rounds based on random sampling from the last Markov iteration
output every II rounds by building consensus from all previous Markov iterations
This option flips alleles in pedigree file according to base pairing (A<-> T and C<->G) if >2 alleles are found when putting pedigree and reference together. Notice that it will not affect A/T or C/G SNPs as strand mismatch won't lead to more than two alleles.