Difference between revisions of "MACH"

From UFRC
Jump to navigation Jump to search
m (Text replacement - "#uppercase" to "uc")
Line 28: Line 28:
 
these estimates.
 
these estimates.
 
<!--Modules-->
 
<!--Modules-->
==Required Modules==
+
==Environment Modules==
===Serial===
+
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
Line 79: Line 69:
 
<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
 
<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
 
__NOTOC____NOEDITSECTION__
 
__NOTOC____NOEDITSECTION__
=Validation=
 
* Validated 4/5/2018
 

Revision as of 13:41, 13 June 2022

Description

mach website  

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.

Environment Modules

Run module spider mach to find out what environment modules are available for this application.

System Variables

  • HPC_MACH_DIR - installation directory
  • HPC_MACH_DIR - executable directory




Citation

If you publish research that uses mach 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.