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MACH 1.0

Description

MACH 1.0 is a Markov Chain based haplotyper. It can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.
Mach was developed by Goncalo Abecasis at the University of Michigan. Mach website.
Mach is intended to be used interactively on Helix. If large numbers of Mach jobs are required (> 2-3 simultaneous jobs), or the jobs are expected to run for a long time, the Biowulf cluster may be more appropriate. Please contact the Helix staff (staff@helix.nih.gov) if you have questions about where to run Mach.

Version

Available versions can be seen by typing 'module avail mach1'.

Sample session

The Mach 1.0 executables can be added to your path with the 'module load mach1' command, which will load the latest executables into your path. If you expect to run Mach frequently, you may want to add 'module load mach1' to your .bashrc or .cshrc file.

The utility FCgene, a format converting tool for genotyped data (e.g. PLINK-MACH, MACH-PLINK) is also available. Type 'module load fcgene' to add the binary to your path, and then 'fcgene' to run it.


helix% module load mach1

helix% mach1 --datfile /usr/local/mach/examples/sample.dat \
    --pedfile /usr/local/mach/examples/sample.ped
Mach 1.0.12 -- Markov Chain Haplotyping
(c) 2005-2007 Goncalo Abecasis, with thanks to Yun Li, Paul Scheet


The following parameters are in effect:

Available Options
       Input Files : --datfile [/usr/local/mach/examples/sample.dat],
                     --pedfile [/usr/local/mach/examples/sample.ped],
                     --mask [0.00]
    Optional Files : --crossoverMap [], --errorMap [], --physicalMap []
       Phased Data : --snps [], --haps [], --hapmapFormat, --autoFlip,
                     --greedy
    Markov Sampler : --seed [123456], --burnin, --rounds
   Mapping Options : --npl, --association
        Haplotyper : --states, --errorRate [1.0e-03], --weighted, --compact
        Imputation : --geno, --quality, --dosage, --mle
      Output Files : --prefix [mach1.out], --phase, --mldetails
    Interim Output : --sampleInterval, --interimInterval

Loaded pedigree with:
    500 individuals to be haplotyped at 46 markers

Formating genotypes and allocating memory for haplotyping
                          Pedigree file ... 114.3 kb
               Haplotyping engine (max) ... 88.6 mb
            Haplotyping engine (actual) ... 88.6 mb
Memory allocated successfully

Found initial haplotype set

Wrote out file [mach1.out.rec] with mosaic crossover rates ...
Wrote out file [mach1.out.erate] with per marker error rates ...

Estimated mismatch rate in Markov model is: 0.00100

helix%

Documentation

MACH tutorial