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16:25, 4 October 2010
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The 1000 Genome pilot project genotypes use NCBI Build 36.
=== Step 1:
For the pre-phasing step we recommend [[MaCH]] using the --phase command line option. As input [[MaCH]] needs a [[Merlin]] format pedigree and data file. All markers must be ordered according to their physical position.
==== Usage ====
mach1 -d sample.dat -p sample.ped --rounds 20 --states 200 --phase --interim 1 --sample 1 --compact
==== Parameters ====
how many iterations of the Markov sampler should be run.
use a random subset of ST haplotypes as reference. We recommend values between 200 - 500. More states result in more accurate haplotypes, but are computational more expensive.
output a set of best-guess haplotypes every I rounds by building consensus from all previous Markov iterations. These haplotypes can be used for imputation.
output a set of haplotypes every SA rounds based on random sampling from the last Markov iteration. These intermediate results can be combined and used as input for the imputation process.
enables [[MaCH]] phasing mode.
reduces the amount of memory needed dramatically, but doubles execution time.
=== Step 2: Imputation ===
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