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== Getting Started ==
=== Estimating Haplotypes for Your Sample === For the pre-phasing haplotyping step , we current recommend using [[MaCH]] using with the --phase command line option. As input [[MaCH]] needs a will need [[Merlin]] format pedigree and data filefiles. All markers must should be ordered according to their physical positionand alleles should be labeled on the forward strand.
==== Your Own Data ====
Within each file, markers should be stored by chromosome position. Alleles should be stored in the forward strand and can be encoded as 'A', 'C', 'G' or 'T' (there is no need to use numeric identifiers for each allele).
==== Parameters Running 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 --compact 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 MaCH website):
{| class="wikitable" border="1" cellpadding="2"
| Number of haplotypes to consider during each update. Increasing this value will typically lead to better haplotypes, but can dramatically increase computing time and memory use. A value of 100 - 400 is typical.
|-
| <code>--rounds 5020</code>
| Iterations of the Markov sampler to use for haplotyping. Typically, using 20 - 100 rounds should give good results. To obtain better results, it is usually better to increase the <code>--states</code> parameter.
|-
| <code>--interim 5</code>
| Request that intermediate results should be saved to disk periodically. These will facilitate analyses in case a run doesn't complete.
|-
| <code>--phase</code>
|}
=== Step 2: Imputation into Phased Haplotypes ===Imputing genotypes using '''minimac''' is an easy straightforward process: after selecting a set of reference haplotypes (see below how to get the latest 1000 Genomes reference panel ready to go with '''minimac''' ), plugging-in the target haplotypes from the pre-phasing step and setting the number of rounds to use for the model parameter estimation, samples get imputed once a second.
Imputing genotypes using '''minimac''' is an easy straightforward process: after selecting a set of reference haplotypes, plugging-in the target haplotypes from the previous step and setting the number of rounds to use for the model parameter estimation, imputation should proceed rapidly.
==== Reference Haplotypes Running Minimac ====
{| class="wikitable" border="1" cellpadding="2"
| Optionally, a string that is used to help generate output file names.
|}
==== Reference Haplotypes ====
Reference haplotypes generated by the 1000 Genomes project and formatted so that they are ready for analysis are available from the [http://www.sph.umich.edu/csg/abecasis/MACH/download/1000G-2010-06.html MaCH download page]. The most recent set of haplotypes were generated in June 2010 by combining genotype calls generated at the Broad, Sanger and the University of Michigan. In our hands, this June 2010 release is substantially better than previous 1000 Genome Project genotype call sets.
== Related Pages ==
