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Minimac: 1000 Genomes Imputation Cookbook

46 bytes added, 19:24, 27 August 2012
Pre-phasing - MaCH
mach1 -d chr1.dat -p chr1.ped --rounds 20 --states 200 --phase --interim 5 --sample 5 --prefix chr$chr.haps
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. A summary description of these parameters follows (but for a more complete description, you should go to the [http://www.sph.umich.edu/csg/abecasis/MaCH/ MaCH website]):
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