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./mach1 -d sample.dat -p sample.ped --rounds 20 --states 50 --phase --interim 5 --sample 5 --prefix sample.pp | tee mach.log
./mach1 -d sample.dat -p sample.ped --rounds 20 --states 50 --phase --interim 5 --sample 5 --prefix sample.pp | tee mach.log
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]):
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]):
./minimac --refHaps hapmap.hap --refSnps hapmap.snps --haps sample.pp.gz --snps sample.snps --prefix sample.imp | tee minimac.log
./minimac --refHaps hapmap.hap --refSnps hapmap.snps --haps sample.pp.gz --snps sample.snps --prefix sample.imp | tee minimac.log
A detailed description of all minimac options is available [[Minimac Command Reference|elsewhere]]. Here is a brief description of the above parameters:
A detailed description of all minimac options is available [[Minimac Command Reference|elsewhere]]. Here is a brief description of the above parameters:
