Changes

From Genome Analysis Wiki
Jump to: navigation, search

Minimac

12 bytes added, 02:19, 12 October 2010
Parameters
==== Parameters ====
--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.
|-
| <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.
|}
== Related Pages ==

Navigation menu