Changes

== Getting Started ==

== Getting Started ==

Download [http://www.sph.umich.edu/csg/abecasis/MaCH/download/ MaCH] and [http://genome.sph.umich.edu/wiki/Minimac#Download Minimac] or [http://genome.sph.umich.edu/wiki/Minimac2#Download Minimac2]. Furthermore, example data used in this tutorial can be found [http://www.sph.umich.edu/csg/cfuchsb/minimac2_example.tgz here]

Download [http://csg.sph.umich.edu/abecasis/MaCH/download/ MaCH] and [http://genome.sph.umich.edu/wiki/Minimac#Download Minimac] or [http://genome.sph.umich.edu/wiki/Minimac2#Download Minimac2]. Furthermore, example data used in this tutorial can be found [http://csg.sph.umich.edu/cfuchsb/minimac2_example.tgz here]

== Minimac and Minimac2 Imputation ==

== Minimac and Minimac2 Imputation ==

  ./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 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]):

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://csg.sph.umich.edu/abecasis/MaCH/ MaCH website]):

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

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

|-  

|-  

|style=white-space:nowrap|<code>-d sample.dat</code>

|style=white-space:nowrap|<code>-d sample.dat</code>

| Data file in [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html Merlin format]. Markers should be listed according to their order along the chromosome.

| Data file in [http://csg.sph.umich.edu/abecasis/Merlin/tour/input_files.html Merlin format]. Markers should be listed according to their order along the chromosome.

|-  

|-  

| <code>-p sample.ped</code>

| <code>-p sample.ped</code>

| Pedigree file in [http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html Merlin format]. Alleles should be labeled on the forward strand.

| Pedigree file in [http://csg.sph.umich.edu/abecasis/Merlin/tour/input_files.html Merlin format]. Alleles should be labeled on the forward strand.

|-

|-

| <code>--states 200</code>

| <code>--states 200</code>