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12 bytes added, 02:19, 12 October 2010
==== Parameters ====
--refHaps ref.hap
Reference haplotypes (e.g. [ MaCH download page])
--refSnps ref.snps
Reference SNPs (e.g. [ 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.
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 [ 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.
| <code>--haps target.hap</code>
| Phased haplotypes where missing genotypes will be imputed.
| --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.
| --prefix imputed
| Optionally, a string that is used to help generate output file names.
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