Changes

  ./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 50 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]):

{| class="wikitable" border="1" cellpadding="2"

{| class="wikitable" border="1" cellpadding="2"

| Reduce memory use at the cost of approximately doubling runtime.

| Reduce memory use at the cost of approximately doubling runtime.

|}

|}

=== Imputation into Phased Haplotypes - minimac ===

=== Imputation into Phased Haplotypes - minimac ===