MACH (version 0.1)

Input files

Input file 1

Input data file (-d):

Specify here the input data file, in linkage or QTDT format.

Pedigree file (-p):

Specify here the pedigree file, with genotype, phenotype and family structure information.

Empirically assess quality of the solutions (--mask):

This option hides a small proportion of genotypes from the haplotyper and then compares the imputed genotypes at these locations with the actual genotypes.

(--crossoverMap):

(--errorMap):

(--physicalMap):

Reference haplotypes (-h):

List of SNPs in the reference haplotypes (-s):

(--hapmapFormat):

(--vcfReference):

(--autoFlip):

(--greedy):

(--startposition):

(--endposition):

Select a seed (--seed):

Selects a different random sequence for simulation and sampling of haplotypes.

(--burnin):

Number of iterations to run the Markov sampler (--rounds):

Larger numbers will result in better solutions. If there isn't much missing data, a value of 50 should give a reasonable solution. Larger values will provide even better solutions.

Whittemore and Halpern NPL all statistic (--npl):

Use the Whittemore and Halpern NPL all statistic to test for allele sharing among affected individuals. Also calculates a LOD score using the Kong and Cox linear model.

Variance component model (--association):

This option uses a variance component model to estimate an additive effect for each SNP and carry out an association test. Before evaluating evidence for association, missing genotypes are estimated to increase power.

Number of haplotypes considered when updating each individual (--states):

Larger values will generate more accurate solutions, but may slow things down a bit (as well as requiring more memory). A value of 200 or larger typically provides quite good solutions. The default is to use all available haplotypes for each update.

(--errorRate):

Use individuals with more genotype data as templates for haplotyping other individuals (--weighted):

Reduce memory use (--compact):

(--forceImputation):

Infer genotypes at untyped markers (--geno):

(--quality):

(--dosage):

(--probs):

(--mle):

Request the output of phased chromosomes (--phase):

(--uncompressed):

(--mldetails):

(--sampleInterval):

(--interimInterval):

What it does

MACH is a Markov Chain based haplotyper. It can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals. The current version is a pre-release.

License and citation

You can use this tool only if you agree to the license terms of: MACH.

If you use this tool, please cite: