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, 22:35, 28 June 2010
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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 |
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| + | == autoflip == |
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| + | 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. |