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output every II rounds by building consensus from all previous Markov iterations
output every II rounds by building consensus from all previous Markov iterations
== autoflip ==
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.
