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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.
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.
==== Usage ====
minimac --refHaps ref.hap.gz --refSnps ref.snps.gz --haps target.hap.gz --snps target.snps.gz --rounds 10
==== 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 R
how many iterations should be run to estimate the model parameters: (i) error rate for each marker (*.erate) and (ii) crossover rates (*.rec) for each interval.
--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
