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, 10:45, 25 May 2010
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| Equivalently, you could write -d reference.dat,sample.dat -p reference.ped,sample.ped on the command line and MACH would merge both files ''on-the-fly''. | | Equivalently, you could write -d reference.dat,sample.dat -p reference.ped,sample.ped on the command line and MACH would merge both files ''on-the-fly''. |
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− | === '''How long does imputation take?''' === | + | === '''How long does imputation take?''' === |
− | A: The following factors/parameters affect computational time:
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| + | A: The following factors/parameters affect computational time: |
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| + | #m, # of genotyped markers (number of markers in .dat file)<br> |
| + | #n, # of individuals<br> |
| + | #h, # of reference haplotypes (determined by --greedy or states, by default, h = 2*number diploid individuals - 2 + number_haplotypes)<br> |
| + | #r, # of rounds (-r or --rounds, --mle corresponds to 1-2 rounds) |
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| + | Computational time increases linearly with m, n, r and quadratically with h. On our Xeon 3.0GHz machine, imputation with m=25K, n=250, h=120, and r=100 takes ~20 hours. <br> |
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| + | <br> |
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| === '''More questions?''' === | | === '''More questions?''' === |