Difference between revisions of "MaCH Options"
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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. | ||
Latest revision as of 22:35, 28 June 2010
greedy
use only the reference haplotypes (fed to -h or --haps) as reference
states S
use a random subset of S haplotypes as reference
sampleInterval SI
output every SI rounds based on random sampling from the last Markov iteration
interimInterval II
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.
