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Revision as of 22:59, 10 February 2011
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Pre-phasing / 2-Step imputation starts with the pre-phasing of your genotypes using MaCH. A typical MaCH command line to estimate phased haplotypes might look like this:
Pre-phasing / 2-Step imputation starts with the pre-phasing of your genotypes using MaCH. A typical MaCH command line to estimate phased haplotypes might look like this:
mach1 -d sample.dat -p sample.ped --rounds 20 --states 200 --phase --interim 5 --sample 5
mach1 -d chr1.dat -p chr1.ped --rounds 20 --states 200 --phase --interim 5 --sample 5
This will request that MaCH estimate haplotypes for your sample, using 20 iterations of its Markov sampler and conditioning each update on up to 200 haplotypes.
This will request that MaCH estimate haplotypes for your sample, using 20 iterations of its Markov sampler and conditioning each update on up to 200 haplotypes.
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You should be able to run this step in parallel and in our cluster we'd use:
<source lang="text">
foreach chr (`seq 1 22`)
runon -m 4096 mach -d chr$chr.dat -p chr$chr.ped --rounds 20 --states 200 --phase --interim 5 --sample 5
end
</source>
=== Imputation into Phased Haplotypes - minimac ===
=== Imputation into Phased Haplotypes - minimac ===
