View source for MACH

[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|mach}}
|{{#vardefine:url|http://www.sph.umich.edu/csg/abecasis/MACH}}
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Genome-wide association studies (GWAS) can identify common alleles that
contribute to complex disease susceptibility. The effects of most common
SNPs must be evaluated indirectly using either genotyped markers or
haplotypes thereof as proxies. MACH software implements a computationally
efficient Markov Chain framework for genotype imputation and haplotyping.
The approach describes sampled chromosomes as mosaics of each other and uses
available genotype and shotgun sequence data to estimate unobserved
genotypes and haplotypes, together with useful measures of the quality of
these estimates.
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==Required Modules==
===Serial===
* {{#var:app}}
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==System Variables==
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{uc:{{#var:app}}}}_DIR - executable directory
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{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
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{{#if: {{#var: exe}}|==Additional Information==
WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
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{{#if: {{#var: pbs}}|==PBS Script Examples==
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.
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{{#if: {{#var: policy}}|==Usage Policy==
WRITE USAGE POLICY HERE (Licensing, usage, access).
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{{#if: {{#var: testing}}|==Performance==
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{{#if: {{#var: faq}}|==FAQ==
*'''Q:''' **'''A:'''|}}
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{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{#var:app}} you have to cite it as follows:

Li Y, Willer CJ, Ding J, Scheet P and Abecasis GR (2010) MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol 34:816-834.
      
Li Y, Willer CJ, Sanna S and Abecasis GR (2009) Genotype Imputation. Annu Rev Genomics Hum Genet 10:387-406.
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{{#if: {{#var: installation}}|==Installation==
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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=Validation=
* Validated 4/5/2018