Difference between revisions of "ProbABEL"
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Genomics]][[Category:Biology]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|probabel}} | |{{#vardefine:app|probabel}} | ||
|{{#vardefine:url|http://www.genabel.org/packages/probabel}} | |{{#vardefine:url|http://www.genabel.org/packages/probabel}} | ||
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
| − | |{{#vardefine:conf|}} <!--CONFIGURATION--> | + | |{{#vardefine:conf|1}} <!--CONFIGURATION--> |
|{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | ||
|{{#vardefine:job|}} <!--JOB SCRIPTS--> | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | ||
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|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
|{{#vardefine:faq|}} <!--FAQ--> | |{{#vardefine:faq|}} <!--FAQ--> | ||
| − | |{{#vardefine:citation|}} <!--CITATION--> | + | |{{#vardefine:citation|1}} <!--CITATION--> |
|{{#vardefine:installation|}} <!--INSTALLATION--> | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
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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}}}}_CONF - sample config file directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
| − | + | Copy the $HPC_PROBABEL_CONF file to your working directory. Edit the resulting '<code>probabel_config.cfg</code>' configuration file before trying to run the analysis. | |
|}} | |}} | ||
<!--Run--> | <!--Run--> | ||
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If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} you have to cite it as follows: | ||
| − | + | Aulchenko YS, Struchalin MV, van Duijn CM. [http://www.ncbi.nlm.nih.gov/pubmed/20233392 ProbABEL package for genome-wide association analysis of imputed data]. BMC Bioinformatics. 2010 Mar 16;11:134. doi: 10.1186/1471-2105-11-134. PubMed PMID: 20233392; PubMed Central PMCID: PMC2846909. | |
|}} | |}} | ||
Latest revision as of 19:35, 21 August 2022
Description
Genome-wide association analysis of imputed data. ProbABEL software package is used for the analysis of genome-wide imputed SNP data and quantitative, binary, and time-till-event outcomes under linear, logistic, and Cox proportional hazards models, respectively. For quantitative traits, the package also implements a fast two-step mixed model-based score test for association in samples with differential relationships, facilitating analysis in family-based studies, studies performed in human genetically isolated populations and outbred animal populations.
Environment Modules
Run module spider probabel to find out what environment modules are available for this application.
System Variables
- HPC_PROBABEL_DIR - installation directory
- HPC_PROBABEL_BIN - executable directory
- HPC_PROBABEL_CONF - sample config file directory
Configuration
Copy the $HPC_PROBABEL_CONF file to your working directory. Edit the resulting 'probabel_config.cfg' configuration file before trying to run the analysis.
Citation
If you publish research that uses probabel you have to cite it as follows:
Aulchenko YS, Struchalin MV, van Duijn CM. ProbABEL package for genome-wide association analysis of imputed data. BMC Bioinformatics. 2010 Mar 16;11:134. doi: 10.1186/1471-2105-11-134. PubMed PMID: 20233392; PubMed Central PMCID: PMC2846909.