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Minimac (view source)

Revision as of 03:19, 12 October 2010

12 bytes added ,  03:19, 12 October 2010
→‎Parameters
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==== Parameters ====
 
==== Parameters ====
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--refHaps ref.hap
  −
Reference haplotypes (e.g. [http://www.sph.umich.edu/csg/abecasis/MACH/download/1000G-2010-06.html MaCH download page])
  −
--refSnps ref.snps
  −
Reference SNPs (e.g. [http://www.sph.umich.edu/csg/abecasis/MACH/download/1000G-2010-06.html MaCH download page])
  −
--haps target.hap
  −
Target haplotypes (from the pre-phasing step)
  −
--snps target.snps
  −
Target snps (from the pre-phasing step)
  −
--rounds [5]
  −
how many rounds should be run to optimize the model parameters: (i) error rate for each marker (*.erate) and (ii) crossover rates (*.rec) for each interval.
  −
--states [200]
  −
how many haplotypes to use for parameter optimization.
  −
--em
  −
use an e-m algorithm, instead of mcmc, for parameter optimization
  −
--rec file.rec
  −
use crossover rates from this file
  −
--erate file.erate
  −
use error rates from this file
  −
--prefix [minimac]
  −
prefix for output files, default minimac
      +
{| class="wikitable" border="1"
 +
|-
 +
! Parameter
 +
! Description
 +
|-
 +
| <code>--refSnps ref.snps</code>
 +
| List of SNPs in the reference panel
 +
|-
 +
| <code>--refHaps ref.hap</code>
 +
| Reference haplotypes (e.g. from [http://www.sph.umich.edu/csg/abecasis/MACH/download/1000G-2010-06.html MaCH download page])
 +
|-
 +
| <code>--snps target.snps</code>
 +
| SNPs in phased haplotypes. These should largely be a subset of the SNPs in the reference panel.
 +
|-
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| <code>--haps target.hap</code>
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| Phased haplotypes where missing genotypes will be imputed.
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|-
 +
| --rounds 5
 +
| Rounds of optimization for model parameters, which describe population recombination rates and per SNP error rates.
 +
|-
 +
| --states 200
 +
| Maximum number of reference (or target) haplotypes to examined during parameter optimization.
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|-
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| --prefix imputed
 +
| Optionally, a string that is used to help generate output file names.
 +
|}
    
== Related Pages ==
 
== Related Pages ==
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/2210"

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