Difference between revisions of "Alphaimpute"
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DOC - documentation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_EXE - example directory |
<!--Configuration--> | <!--Configuration--> | ||
Revision as of 21:11, 6 December 2019
Description
AlphaImpute is a software package for imputing and phasing genotype data in populations with pedigree information available. The program uses segregation analysis and haplotype library imputation to impute alleles and genotypes. A complete description of the methods is given in Hickey et al. (2012). AlphaImpute consists of a single program however it calls both AlphaPhase1.1 (Hickey et al., 2011) and GeneProbForAlphaImpute (Kerr and Kinghorn, 1996). All information on the model of analysis, input files and their layout, is specified in a single parameter file.
Environment Modules
Run module spider alphaimpute to find out what environment modules are available for this application.
System Variables
- HPC_ALPHAIMPUTE_DIR - installation directory
- HPC_ALPHAIMPUTE_BIN - executable directory
- HPC_ALPHAIMPUTE_DOC - documentation directory
- HPC_ALPHAIMPUTE_EXE - example directory